The Boeing 737, operated by Miami Air International, ended up in a river after landing during a thunderstorm.
Officials said 21 people were taken to hospital with minor injuries, and at least four pets kept in the hold died.
They are now looking into the failure of the "thrust reverser", as well as a request by the pilot to change runways.
The flight, which had flown from Guantanamo Bay in Cuba to a military base in the city of Jacksonville, is said to have landed heavily in the storm before skidding into St John's River.
The 136 passengers and seven crew members on board evacuated the Boeing 737-800 via its wings.
Investigators have obtained the flight data recorder but the cockpit voice recorder remains in a submerged area of the plane.
Authorities must wait until the remaining fuel - around 1,200 gallons (4,500L) - is removed before attempting to salvage any evidence.
"The aircraft had been in maintenance and the maintenance log noted that the left hand thrust reverser was inoperative," Bruce Landsberg, vice-chairman of the US National Transportation Safety Board, told a press conference on Sunday.
Mr Landsberg added that shortly before they landed, the pilots had asked to change to a runway which had equipment set up on it, and which therefore had less space available.
"We don't know what they were thinking or why that was their choice," he said.
On Sunday, the Naval Air Station
in Jacksonville confirmed that the bodies of a dog and two cats were recovered from the aircraft. Another animal that had travelled in the cabin was removed alive by its owner.
'Terrifying' moment
One passenger on the plane, Cheryl Bormann, described the "terrifying" moment it slid off the runway.
"The plane literally hit the ground and bounced - it was clear the pilot did not have total control of the plane, it bounced again,".
"We were in the water. We couldn't tell where we were, whether it was a river or an ocean," she said, adding that she could smell jet fuel leaking into the river.
In a news conference, Captain Michael Connor, commanding officer at Naval Air Station Jacksonville, said it was a "miracle" that there had been no serious injuries or fatalities.
Miami Air International is contracted by the US military for its twice-weekly "rotator" service between the US mainland and Guantanamo Bay, Bill Dougherty, a base spokesman said.
Officials say the people on Friday's flight included civilian and military personnel.
Boeing released a statement sharing its "well wishes" with those on board.
It said it was providing technical assistance to the US National Transportation Safety Board, which is investigating the incident.
The aerospace giant has been under increased scrutiny following two fatal crashes involving its 737 Max 8 planes - a different model to the one involved in the incident on Friday.