Public broadcaster SVT said the plane was stopped on the tarmac as it was about to take off from the northern Swedish town of Luleå, and Peter Hultqvist was whisked off.
SVT cited passengers on board the flight who recognized the minister and a police investigator who confirmed he was booked on the flight.
The Swedish government and his security detail refused however to confirm whether Hultqvist was indeed on board.
“We don't disclose schedules or any details of our travel arrangements,” said defence ministry spokesperson Marinette Nyh Radebo.
Other passengers were also taken off the flight and police said in a statement they had responded to a threat called in to the Luleå airport, but they deemed it a hoax and called off their response.
“It's a youthful voice anyway. They interpreted it as a quote 'prank call', it sounded like a guy but we don't know for sure,” said police investigator Inge Bars.