Jakarta – Three bodies were found and some 40 people were missing and feared dead after an attack on a boat carrying Muslims from Indonesia's Ternate island to a port in northern Halmahera, a port official said Thursday.

"Three bodies and 15 survivors have been found so far and six of the survivors were injured, some with bullet wounds," said a staff member of the port administration in Bastiong on Ternate island, which is part of the Northern Maluku province.

"Forty other people are still missing and although search efforts are continuing we have little hope that they are still alive," said the staff member, who identified himself only as Udin.

He said the Hasil Karya-2 motorized sailboat had left the port of Bastiong on December 7, and that four days later the port was notified that the boat never reached its destination in Kahatola island in Loloda Bay some 100 kilometres north of Ternate.

All the people on board the ship were Muslims, Udin said, and the first survivor, found by fishermen in Loloda Bay on December 11, spoke of the boat sinking after it was rammed and attacked by a tugboat on December 7.

"The tugboat, which was manned by Christians, had forced the Hasil Karya-2, to enter the Loloda Bay instead of going to Kahatola," a small island in front of the bay, Udin said.

When the captain refused, the tugboat rammed the ship and a volley of shots and arrows were fired from the tugboat. "The captain's son, who was among those found injured and currently being treated at the hospital, has bullet wounds on his right hand," Udin said.

He said the search for those missing involved ships from the naval base in Ternate as well as fishing boats from the Loloda area.

A probe team has been sent to the area by the governor, the administrator of the State of Civil Emergency imposed on North Maluku in June following more than a year of bitter and violent Muslim-Christian conflict there, the Antara news agency said.

The probe team, headed by an army major, arrived in Kahatola on Tuesday, Antara said. The agency also said that nine people were confirmed killed in the attack, but added that only three bodies had been buried so far.