An investigation is underway following a deadly collision between a Japan Airlines flight and a Coast Guard aircraft at Tokyo's Haneda Airport on Tuesday.

Five crew members aboard the Coast Guard aircraft, which was helping with earthquake relief efforts, were killed while all 379 passengers aboard the Japan Airlines plane were safely evacuated.

Four passengers were later transported to a local hospital. The captain of the Coast Guard aircraft escaped but is in critical condition.

"We apologize for any inconvenience and concern this may have caused to our customers and all concerned. We pray for the rest of the souls of those who lost their lives aboard the Japanese Coast Guard's equipment and extend our condolences to the bereaved families," Senior Vice President of Japan Airlines Noriyuki Aoki said in a statement.

"We will provide accompany service to those who have come to Haneda to meet their families."

According to Tadayuki Tsutsumi, Japan Airlines' senior vice president of corporate safety and security, preliminary reports are that the Japan Airlines flight was confirmed to have "entered the runway as normal and began landing as normal and that there was an impact, which led to the accident, but we are still investigating further details."

"However, I can't say at this time if they [Japan Airlines aircraft] were cleared to land, or if they communicated with ATC, because that is a fundamental factor in the cause of the accident, and we are still trying to confirm that," Aoki said during a news conference on Tuesday.

The crash marks the first time that an Airbus A350 has been severely damaged. The large aircraft entered commercial service less than a decade ago.

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