The Boeing 737-800 was carrying a total of 47 people, including 36 passengers and 11 crew members, Emilio said.
Air Niugini is Papua New Guinea's national airline.
None of the 35 passengers and 12 crew onboard flight ANG73 suffered serious injuries.More news: Google celebrates 20 years, walks down memory lane
The flight from Pohnpei, Micronesia, to Chuuk usually takes about one hour.
Passengers can be seen evacuating the submerged aircraft.
It was stationary at the Jacksons International airport when a cargo plane clipped its wing while turning, according to PNG's Accident Investigation Commission.
Locals rushed out to the scene of the crash on small boats to help rescue passengers, who escaped the aircraft and were standing on the wings.More news: Thai universities drop in world rankings
"I thought we landed hard until I looked over and saw a hole in the side of the plane and water was coming in", passenger Bill Jaynes said in a video posted by the Pacific Daily News website.
"On a normal landing you end up 30m from the end of the runway and the end of the runway means water", he said.
Reports of an Air Niugini 737 overrunning the runway in Chuuk, Micronesia (TKK).
Papua New Guinea authorities have confirmed that an Air Niugini plane has overshot a runway in Micronesia and ended up in the ocean.More news: Chinese Media: Trump Election Allegations 'Crazy Talk,' 'Creative Strategy'
"It landed in the water about 160 yards [145 metres] off shore".