This wouldn't be a copyright issue. Copyright is broadly about protecting the ownership of artistic works from unauthorised "borrowing" (or "sampling", as glo-stick waving, bug-eyed fans of plink plink electronica would probably call it)..
Referring to something which exists therefore isn't the same as infringing copyright, at least not in Blighty. So, if your characters are in a pickle with HMRC (Her Majesty's Revenue and Customs) for failing to pay their income tax or for failing to declare brown envelopes stuffed with used twenties, you are not under any obligation to rename HMRC "the British Tax Authority".
Same goes for the Sea Scouts, the RAC, The Department of Work and Pensions, the Duchy of Lancaster and the Dagenham Girl Pipers*.
What you can't do is defame folk. Defamation isn't always that easy to prove - but some organisations (notably big commercial interests) are long on pocket and short on sense of humour.
Regards,
Peter
* Less suntanned than cheerleaders and with less blinding smiles and considerably Worse Hair, but they'd hold the line against zombie apocalypse with grace and aplomb.