The crash forced the airport to shut down all runways for several hours on Tuesday evening, leading to cancellations of 226 flights to and from Haneda, affecting over 40,000 passengers.

Despite the reopening of three runways on Wednesday, about 100 flights are still expected to be scrubbed on the day, disrupting the travel plans of 19,000 passengers.

At around 6 p.m. local time on Tuesday, Japan Airlines (JAL) Flight 516, an Airbus A-350 that had flown from New Chitose Airport in Hokkaido Prefecture was landing on Handa's C-runway when the Coast Guard flight MA-722, a Bombardier Dash-8, collided with it, with both aircraft catching fire.

Television footage on Tuesday showed a large burst of fire erupting from the side of the JAL plane as it taxied on a runway. The area around the wing then caught fire. The footage seen an hour later showed the blaze engulfed the aircraft.

Five of the six crew members aboard the MA-722 were confirmed dead, while the captain who managed to escape earlier was severely injured.

The flight was cleared to land

According to The Japan Times, at 5:43 p.m. local time, control-tower staff told pilots of the Airbus A350-900 jet to continue their approach into Haneda. A minute and a half later, the flight was given clearance to land, according to audio posted on LiveATC.net, which tracks airport communications, reported the daily.

However, all 367 passengers and 12 crew members on board the JAL flight escaped from the airplane while it was on fire without life-threatening injuries after the collision.

The Tokyo Fire Department said it took more than eight hours to extinguish the fire following the crash.

A Haneda air traffic controller had permitted the passenger plane to land on a runway before the crash took place, and had ordered the coast guard aircraft to "hold short of the runway," national broadcaster NHK reported, citing sources with Japan's transport ministry.

The Japan Transport Safety Board, the government-affiliated agency in charge of probing serious accidents involving airplanes, trains and ships, on Wednesday started investigating the cause of the accident and examining the aircraft wreckage.