Two 16-year-old Japanese nationals have drowned on Fraser Island, north of Brisbane.

Key points: The boys were reported missing from a school tour group near Lake McKenzie just after 5:00pm on Friday

The boys were reported missing from a school tour group near Lake McKenzie just after 5:00pm on Friday Their bodies were found in the water at Lake McKenzie about 8:20am on Saturday

Their bodies were found in the water at Lake McKenzie about 8:20am on Saturday The boys' families have been notified and police are working very closely with the Japanese consulate

Queensland police said the boys were reported missing from a school tour group near Lake McKenzie just after 5:00pm on Friday.

Local officers, swift-water rescue crews, State Emergency Service officers and the Rural Fire Service and helicopters were involved in the search at Fraser Island.

The bodies of the two boys were found in water about 8:20am on Saturday.

Police will prepare a report for the Coroner.

Police Inspector Tony Clowes from the Maryborough Patrol Group said the boys had been on the same school tour together.

Inspector Clowes said the boys' families had been notified and police were working very closely with the Japanese consulate to provide all the support it could to the families.

He said police were in the early stages of their investigation.

"This is a tragic event — there is no doubt about that," Inspector Clowes said.

Two bodies were found on Saturday morning at Lake McKenzie. ( ABC News: Ellie Sibson )

"Certainly it would be confronting for all persons involved, including emergency services who responded.

"There'll be a full investigation — obviously we'll be speaking to all the witnesses available and putting together a full picture of exactly what occurred, the events, and the timing of the events."

The boys were on a high school exchange. They left Japan on March 24 and were planning to return on the 31st.

Their school was informed by police on Saturday morning. The boys' families and vice principal of the school are travelling to Brisbane.

Jeff Ellison from SeaLink Travel Group, which owns Kingfisher Bay resort, said staff were cooperating with police as part of the investigation.

"They were on a group tour with guides with them and interpreters," Mr Ellison said.

"We're doing an investigation and obviously cooperating with the police who are leading the investigation to see what happened.

"Our whole team up there is deeply saddened about this tragic event and at the moment out thoughts are with the families and friends."

Fraser Coast Mayor George Seymour said the deaths had shocked the community.

"Lake McKenzie is the postcard-perfect image of Fraser Island — it's where all the tourists go," Cr Seymour said.

"It's really unimaginable how somebody, let alone two people, could drown there."

Cr Seymour said the popular tourist spot was considered a very safe place.

"It's a calm lake in the middle of an island … whatever has happened is highly unusual," he said.