All 18 air controllers on duty at Tokyo's Haneda Airport forgot a runway was shut for construction and one of them told a plane to land there, officials said, but the aircraft was safe as the stretch was clear.

The incident, days after Japan's worst train crash in 40 years killed 106 people, raised questions about safety in a country that prides itself for its efficient transport system.

The Japan Airlines plane with 51 passengers and crew landed at the mainly domestic Haneda Airport on Friday according to directions given by the controller, a Transport Ministry spokesman said.

"The controller had not worked since the runway was closed for construction at the beginning of April, and forgot that it had been closed," the spokesman said, adding that there was no construction equipment on the runway when the plane landed.

"All 18 of the controllers working at that time had forgotten," he said.

All of them will be sent for re-training for at least a week to prevent a recurrence, and Japan's domestic airports will be told to take another look at their safety procedures.

Japan Airlines has recently suffered from a spate of mistakes, including a pilot incorrectly hearing instructions from air traffic controllers, which led the transport ministry to tell the airline it would have to take more care.