'Tiger King' star Joe Exotic allegedly managed to have a helicopter fly over his old zoo and freak out all the animals -- at least that's what Joe's ex-business partner and owner of the zoo, Jeff Lowe, thinks ... but Joe's team is calling BS.

According to the FAA ... it received an official complaint about a chopper illegally flying over Lowe's Greater Wynnewood Exotic Animal Park Sunday afternoon in Oklahoma. We're told an investigation is underway.

Sources close to Jeff tell TMZ ... the helicopter violated restricted air space and at one point was hovering right over the zoo's gift shop. We're told this caused the animals to go nuts and stressed out the endangered ones, which violates the Endangered Species Act.

As for the connection to Exotic ... our sources say Lowe's people got the chopper's tail number as it buzzed nearby, and discovered it matches with the one featured in a video produced by Joe's legal team.

We broke the story ... the legal team made the video to ask President Trump to free Joe, claiming he was framed for putting a hit out on his foe, Carole Baskin.

We're told Jeff's wife, Lauren, called and reported the incident Monday to the FAA.

Joe's rep, Eric Love, tells us ... Team Tiger has no knowledge of the incident. Love says no one on the team was involved, and says the helicopter used for the video was one they chartered ... it's not theirs.

Of course, the whole thing raises eyebrows. As you may recall from 'Tiger King' ... Joe once flew a helicopter over Baskin's Big Cat Rescue park in Florida to check it out, which she also claimed caused the animals distress.