According to NBC Nightly News the Star Wars veteran was in a “potentially serious" incident as he was piloting a single-engine private plane on Monday, February 13.
Harrison reportedly tried to land on the tarmac at the John Wayne Airport in Orange County when he came dangerously close to a passenger plane with 110 people on board.
In a statement released to Variety, the FAA explained: "Air traffic controllers cleared the pilot of a single-engine Aviat Husky to land on Runway 20L at John Wayne Airport Monday afternoon. The pilot correctly read back the clearance."
"The pilot then landed on a taxiway that runs parallel to the runway, overflying a Boeing 737 that was holding short of the runway. The FAA is investigating this incident."
In 2015, the actor gave the world a major scare when he made an emergency landing in a vintage WW2 single-engine plane, after it experienced an engine failure.
Harrison was able to land in a nearby golf course in California, but banged up the plane – and himself – in the process. He suffered a broken pelvis and a broken ankle in the 2015 crash.
This marks the actor's fourth major crash in his aviation career. It follows previous crashes in 1999 and 2000, where he escaped unscathed.
Speaking of her husband's hazardous hobby, actress Calista Flockhart says he has her unwavering support.
"He loves it, so I love it, and I support him 100 percent," the former Ally McBeal star explained two years ago during a CBS TCA panel.
"I think it just makes you realise once again that life can turn on a dime, and we just have to appreciate every second we're here, because you never know."
Speaking on the crash itself, Calista revealed to People that it was a "really hard, scary time" for her family, which includes 16-year-old son, Liam.
Despite his poor track record, the star's love of planes has been well documented.
"I have more airplanes than it’s fair for anybody to have," he confessed to Airport Journals back in 2004.
"I love the sound of a round engine. My de Havilland Beaver has a Pratt & Whitney 985 [are my favourites]. It’s a beautiful sound."
In 2014, Harrison had another horrific accident during the filming of Star Wars: The Force Awakens after he was crushed by a door on set and badly injured his ankle and broke his leg.
Harrison is yet to comment on this latest incident.