The US resumed operations with its CH-53 helicopters today, after grounding them for a week following the blaze in an empty field on the western Japanese island of Okinawa.
At the time the US military said the blaze occurred after the aircraft had landed in the field and no crew were injured.
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Japanese Defence Minister Itsunori Onodera told reporters it was "truly regrettable" that the flights had resumed "without enough explanations".
Deputy government spokesman Kotaro Nogami said US officials had briefed their Japanese counterparts but Tokyo was not satisfied and would "continue asking for further explanations from the US side".
Onodera had previously called for the helicopters to be idled until their safety can be guaranteed and dispatched experts to Okinawa to ensure a thorough investigation.
Representatives of the US military in Okinawa could not be reached for immediate comment Wednesday.
More than half the approximately 47,000 American troops in Japan under a decades-long security alliance are stationed on Okinawa, the site of a major World War II battle that was followed by a 27-year US occupation of the island.
Islanders have complained for decades about noise and accidents.
In December, five crewmembers aboard a US Marine MV-22 Osprey were injured after what the Pentagon described as a "mishap" resulting in the plane landing in shallow water off Okinawa.
Okinawa residents have protested against the deployment of Ospreys in Japan after a series of accidents in other countries involving the hybrid aircraft.