The flight from Lagos to Abuja was taxiing on the runway when the emergency exit door came away.
Dana Air denied that it was caused by a mechanical fault, and said the door could not fall off "without a conscious effort by a passenger to open it".
But one passenger told the BBC that everyone on board had denied tampering with the door.
Dapo Sanwo, from Lagos, said: "The flight was noisy with vibrations from the floor panel. I noticed the emergency door latch was loose and dangling."
"When we landed and the plane was taxiing back to the park point, we heard a poof-like explosion, followed by a surge of breeze and noise. It was terrible."
"The cabin crew tried to say a passenger pulled the hatch which everyone denied. They also tried to get us to stop taking videos or pictures."
Ola Brown, who was also travelling on the flight, said on Twitter: "Did you hear [the door] rattling the whole flight? Was so unsettling. I just thought it was a screw loose, Didn't think it would actually just fall off."
In a statement, Dana Air denied there were issues with the door during the flight.
"The emergency exit door of our aircraft are plug-type backed by pressure, which ordinarily cannot fall off without tampering or a conscious effort to open by a crew member or passenger," the company said.
"When an aircraft is airborne, it is fully pressurised and there was no way the seat or door could have been shaking as insinuated."
The airline went on to say it had been inspected by engineers alongside a Nigerian Civil Aviation Authority team and "no issue was reported".
"The [return] flight was only delayed for eight minutes as we needed to demonstrate to the regulators that the safety and comfort of our guests is at the centre of our operations," the statement added.
In 2012, a Dana Air flight crashed in a busy Lagos suburb killing all 153 people on board.
Nigeria has historically had a poor air safety record. Last year, Abuja's airport airport was closed for six weeks while major repairs were carried out on its runway.