I have just finished a mystery in which I have used the name of a real community organization. It's an organization that people either love or hate because it represents the upper echelon of society, presents debutantes every year, etc. I do not trash the group; it is simply a background for a character who is a member of the organization and who is promoting herself to become the leader. She comes across as being cynical and self-centered, but in the end, despite her warts, she redeems herself. I have included a disclaimer indicating that organizations, events, etc. are either the products of the writer's imagination or are used fictitiously. Am I on thin legal ice for not changing the group's name? This mystery will be self-published.
I'm not a lawyer but if it were me I'd feel like I was on thin legal ice.
Even if you don't think you trash them, they might think so, and then sue you for defamation, claiming the worst thing you write about them has damaged their reputation.
Disclaimers are not a bullet proof shield, just because you say it does not give it a presumption of truth in court. Anybody can lie in print.
Suppose you were on a jury, and some author tells you, "The fictional character that I wrote having the same name, address, age, appearance and profession as my real life boss, the one that I portrayed as an embezzler and weekend prostitute, was entirely a figment of my imagination."
Whose side do you take, jury member? Was the author's disclaimer a lie, or do you consider it automatically true just because it was written in a book?
I repeat I am not a lawyer, but to be safe I'd change the name and details. You might even refer to the real name as their competitor and a thorn in their side, so no rational reader would think they are the same organization.
Readers will accept an entirely fictional giant organization or corporation. Using the real name does not add to the story, if anything it is a writing shortcut you should not take.
IANAL disclaimer included by reference.
You should be okay using a real organization as background (Joe had spent nine years in the Army before being wounded and receiving a Medical Discharge), providing they aren't involved in the actual plot. That doesn't seem to be what you're writing, though.
You seem to be writing about the internal politics of an organization, which (to me) means you should be writing about a "different organization" and using the "small penis rule" to ensure they won't sue you because to do so, they'd have to admit they have a small penis. In other words, give your fictional organization one or more features that make it obvious they're not the original they're otherwise patterned after, to which the original would have to confess in order to claim in court they're who you meant.
So, if you want to use CIA, you'd make up another "agency" (Steven King called his "The Shop" in Firestarter), pattern their general operations after CIA (maybe with a little NSA or FBI thrown in), and give them an undesirable trait -- perhaps they infect all their operatives with a virus that they keep in check with periodic injections of an antiviral agent. Then you can include some tension for a rogue agent having to find a way to steal the antiviral, and ensure that the CIA won't admit that you're talking about them in any other way that matters. Might not keep them from killing you, in this case (joking!), but it should keep your out of court (or at least, it's worked that way for other authors).
Unless this organization is iconic, I would spend a few sentences to create and describe your own version of the organization, making it different enough so that you can say with a straight face, not the same, really, never crossed my mind that anyone would be confused.
And by iconic, I mean that this organization, and only this organization, has a lock on a particular set of characteristics that are critical to your story. Then you have no choice. Grit your teeth and accept the fact that the lawyers can sue you for breathing, if they want. Just try to write a story that is so compelling that the iconic organization would be embarrassed to sue you. This assumes that the leadership is rational, an increasingly rare trait these days.
Everything that you do has risk. There will always be someone to object to what you have written, no matter how careful you are. My advise is to write the story that you believe in and do it so well that the beauty of the story overwhelms any of the negative aspects of the story.
So, I would categorize three possible real life organizations:
Government Agency i.e. a Government of a country controls this agency as part of it's administration.
Political Organization i.e. An organization that provides support for politicians in the election process. In non-democratic nations, this could be seen as court or national factions within the ruling single party. Also includes advocacy groups for certain issues.
Private organizations i.e. not controlled by the government or political interests but by private ownership, associations, or publicly traded stocks.
In case one, by all means, use as you see fit. In the United States, all government symbols and names are public domain, so there would be no lawsuit from the agency in question. In addition, since this is critical of an agency of the government, First Amendment Rights will prevent this. Check your local laws on what government agencies copyright status in your own country.
In case two, again, from a US perspective, let's say that the two dominant political parties are The Bull Moose Party and the Prohibition Party... if you write a character in either of those parties, they may not like it, but probably won't do anything about it. However, you could alienate readers if you paint the Prohibition Party as evil even when they're supports think otherwise. If it's not about politics, it's best to make a fictional party or just don't give the party at all (A famous character along the former line is Senator Kelly of X-Men fame. His party is never identified and his single issue he strongly supports is not a real issue, so he's hard to peg down. Pay attention in the X-men films, which include nods that he has both Republican (a news paper says Democrats respond to his speech) and Democratic leanings (He's pro-gun control and from a Democratic leaning state). Similarly, Martha Kent's party is never given despite a pro-immigrant stance (more democrat issue) and coming from a very Republican state (Kansas hasn't voted Democrat to senate since the Depression).). Again, it's not the suit, it's the readership that will get offended at taking shots at your party (or another portraying that party in a good light).
In the Third Case, unless it's window dressing, make your own. For example, if you're going to eat in a fast food burger joint during your seen, there's nothing wrong with saying McDonald's or Burger King... if you're going to comment that the corporation is an evil alien plot... might just call it "King Clown Burger". In the former, eating food is not something the company cares much about because, hey, marketing we didn't pay for is good. In the latter, you aren't marketing... you're accusing. Since this is a mystery novel, and without knowing the original organization, I think the ice is pretty thin... if not downright melting... since the politics must be some part involved in the mystery. As is, the nature of the organization is one that probably has lots of money (which translates to lawyers) and is very niche to the people involved in those things... so it's better to make your own that could sound to the non-initiate like a real organization, can ring a bell to the initiated, and doesn't offend the money... lawyers...
It is legally unproblematic to use institutions that are of a quasi-timeless nature such as the catholic church, the United States, or the egyptian pyramids.
If you have "a president of the USA" in your novel, this person will be understood to be a fictional president and not the current one (unless you make it clear that he is).
Institutions that are perceived to be a part of our present times, on the other hand, will always be identified with their real counterpart.
If you have "Microsoft" in your novel, every reader will understand everything you write about your fictional Microsoft to be representative of your opinion of the real company.
I would therefore always and without exception choose a fictional company, institution, or person.
I agree with most of what others have said. Let me just add:
Unless your goal is to attack this organization, what do you gain by using a real organization?
You're obviously aware of the danger: As someone else said, even if you don't see your portrayal of the group as trashing it, they might. Even if their case is absurd, if they take you to court, you have to pay lawyers to defend yourself, and maybe no matter how absurd you think it is, a judge or jury will agree with them.
So what's the up-side? If the organization is very well known, maybe you can get a short cut on explaining the back story. Like if you write, "Bob went to Kentucky Fried Chicken", you don't have to explain that this is a fast food restaurant that serves chicken. But this can also be a drawback. What if some real fact about this group clashes with what you need for your story? Or what if out of ignorance you make inaccurate statements about the group? Someone who knows more about the group than you do might find your story jarring because you say things that don't make sense. That could be trivia, like, "What? He says the hero visited the president of the group and stood in his office looking out the window?? But the president's office doesn't have any windows ...". Or it could be more substantive. Like I've read stories that talk about groups that I'm a part of and I often find myself saying, "No, that's not why we opposed the XYZ Bill. It had nothing to do with the money, it was all about the ethical issue ..." etc.
You will automatically drag in reader's opinions about the real group. If you talk about, say, the Catholic Church, presumably real Catholics will automatically have positive thoughts and real atheists will have negative thoughts.
And if you use a real group and say anything negative about them at all, you risk alienating potential readers. We live in divisive times. If I open a novel and there's a reference to my religion or a political party, I am instantly on edge. If I'm in the mood for a fun adventure story or an intriguing mystery, I don't want to read a diatribe against things that I believe in. There are times when I am happy to get into a rip-roaring debate, but there are also times when I'd just rather not. I've often tossed books aside because they got into religious or political or social debates that I was just not in the mood for, I wanted to read some light fiction.
Using a real group doesn't really add to the realism of a story. I've never heard someone say, "That movie was totally unbelievable because there is no such company as Wayne Industries. I checked every stock exchange in the country and it's not listed on any of them." Readers of fiction readily accept fictional companies, fictional religions, even entire fictional nations.
I suppose I'd use a real group when it's a group that monopolizes that "area" so that supposing a fictional group could be jarring. Like if I needed to refer to American politics, I might mention Congress and the president, because trying to talk about "the United State Parliament" or the "king of the United States" would be too jarring. Unless this is an alternate history story or something, readers know that the US doesn't have a king and a parliament. But outside of major organs of government, I'm hard pressed to think of examples. I wouldn't balk at a fictional agency within the government. Life if a novel said that the spy worked for the National Intelligence Bureau -- a name I just made up, I don't think there's any such group -- few readers would hesitate over it for a moment.