A passenger jet that collided with a coastguard plane at Haneda airport in Tokyo had been given permission to land, but the smaller plane was not cleared for takeoff, Japanese authorities have said, as police reportedly prepared to investigate whether the crash involved professional negligence. Five people on the coastguard aircraft died but all 379 passengers and crew escaped to safety down emergency slides minutes before the Japan Airlines Airbus was engulfed in flames on Tuesday. Transcripts of air traffic control instructions released by authorities appeared to show the Japan Airlines plane had been given permission to land but that the coastguard aircraft had been told to taxi to a holding point near the runway. An official from Japan’s Civil Aviation Bureau told reporters there was no indication in the transcripts that the smaller aircraft had been granted permission to takeoff. The captain of the plane, who survived the crash, said he had entered the runway after receiving permission, a coastguard official said, while acknowledging there was no indication in the transcripts that he had been cleared to do so. “The transport ministry is submitting objective material and will fully cooperate with the ... investigation to ensure we work together to take all possible safety measures to prevent a recurrence,” the transport minister, Tetsuo Saito, told reporters. Authorities began inspecting the charred wreckage and the runway for clues as Haneda reopened three of its four runways on Wednesday. On the closed runway, the burnt-out husk of the airliner was evidence of just how close the plane came to major disaster. The captain of the coastguard plane – which had been carrying aid to the region affected by the powerful earthquake on New Year’s Day – was its lone survivor, sustaining serious injuries. Footage on Tuesday showed a ball of fire erupting and thick black smoke coming from underneath the airliner shortly after it landed and came to a halt on its nose. Passengers could be seen coming down inflatable slides as flames shot out from the rear of the aircraft in video posted on X. Aviation experts have praised the crew, saying their actions helped avert a far worse outcome. As the plane was evacuated, dozens of fire engines tried to douse the flames but it was soon engulfed and it took eight hours to extinguish the blaze. “As soon as we landed, there was a bang. And I noticed a blaze rising from the right side,” a passenger told NHK. “It was getting hot inside the plane, and, to be honest, I thought I wouldn’t survive.” A woman with a small child said: “I thought we landed normally. But then I realised I was smelling smoke. I looked outside and it was already burning. I needed to protect my daughter. That was the only thing on my mind.” Government officials said there would be an investigation into the incident. Before Tuesday, Japan had not experienced a serious commercial aviation accident for decades. The crash came weeks after the global airline industry was given new warnings about runway safety. Local media reports said police would conduct an investigation into whether possible professional negligence had led to deaths and injuries. A police spokesperson said a special investigation unit had been set up at the airport but declined to comment on whether it was looking into possible professional negligence. Hiroyuki Kobayashi, a former JAL pilot and aviation analyst, said: “There’s a strong possibility this involved human error. Only one plane is generally allowed to enter the runway but even though landing clearance had been given, the Japan coastguard aircraft was on the runway.” Airbus, the company that manufactured the JAL plane, said it would send a team of specialists to help Japanese authorities investigate. Investigators from Britain, where its two Rolls-Royce Trent XWB engines were manufactured, were due to join them. Some domestic flights were operating on Wednesday morning from Haneda, one of the world’s busiest airports, but dozens were cancelled. The passenger plane had arrived from New Chitose airport, serving Sapporo on Japan’s northernmost main island of Hokkaido. Those onboard included eight children. The coastguard plane had been preparing to fly to Ishikawa prefecture to deliver supplies after the earthquake, which killed at least 64 people. The prime minister, Fumio Kishida, praised the coastguard crew who died on their way to help victims of the quake. “These were employees who had a high sense of mission and responsibility for the affected areas,” he said. In 1985, a JAL jumbo jet flying from Tokyo to Osaka crashed in the central Gunma region, killing 520 passengers and crew. It is the world’s deadliest plane crash involving a single flight.