The aircraft, a Boeing 737-800, flew into a lagoon near Chuuk International Airport on Weno island.
Police have confirmed that all 47 who were onboard the plane are safe.
Boeing 737-800 aircraft can hold up to 189 passengers in addition to crew.
These were split between 36 passengers and 11 crew members.
It had been on route to Port Moresby in Papua New Guinea.
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The aircraft overshot the runway whilst landing.
Photos from the scene show the aircraft in the water, with passengers being picked up by boats.
In the pictures the aircraft is partially submerged, but has not sunk.
The aircraft was being operated by Air Niugini, the national carrier of Papua New Guinea.
There are not believed to have been any deaths or serious injuries.
John Merelli, who works at a hotel near the end of the runway, spoke to The Guardian Australia.
He said he heard the aircraft and assumed it was a normal landing, but then he went back to his workplace and somebody told him the plane was starting “to go underwater”.
He added: “It was sinking. It’s under water now.
“The plane crashed and in around five minutes the rescuers were there.
“They were ordinary people because there are plenty of boats around the shore.”
He added that rescue services arrived around 10 minutes later.
Papua New Guinea officials say investigators from the country will head to Micronesia.
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