One Cambodian crew member was rescued four days later by passing fishermen, but 14 other sailors remain missing, Choong said. The maritime bureau received a report on the apparent mistake late Tuesday from Bangkok-based Sirichai Fisheries, which owned the trawler, the Ekawat Nava5, he said.
"The Indian navy assumed it was a pirate vessel because they may have seen armed pirates on board the boat which had been hijacked earlier," Choong said.
India's navy said last week that the INS Tabar, which began patrolling the gulf on Nov. 2, battled a pirate "mother ship" on Nov. 18, setting the vessel ablaze.
In New Delhi, Indian navy spokesman Commander Nirad Sinha said Wednesday that the INS Tabar was responding to threats to attack from pirates on board the ship.
"Insofar as we are concerned, both its description and its intent were that of a pirate ship," he said. "Only after we were fired upon did we fire. We fired in self-defense. There were gun-toting guys with RPGs on it."
Sirichai Fisheries said its information about the battle came from the Cambodian sailor, who is now recuperating at a hospital in Yemen, said Wicharn Sirichaiekawat, the company's managing director.
"We are saddened with what has happened. It's an unfortunate tragedy. We hope that this incident won't affect the anti-piracy operation by the multi-coalition navies there," Choong added.
Warships from Denmark, India, Malaysia, Russia, the U.S. and NATO patrol the vast international maritime corridor, escorting some merchant ships and responding to distress calls in the area.
The Thai foreign ministry said it was investigating whether the Indian ship correctly followed the rules of engagement and was reviewing reports from the Thai Embassy in New Delhi, the International Maritime Bureau and coalition forces patrolling the waters.
The ministry was also seeking more information on the missing sailors, it said in a statement.
Sirichaiekawat said his company had contacted the International Maritime Bureau after getting messages from other boats in the region that the Ekawat Nava5 had been attacked by pirates.
Sirichai Fisheries asked if any naval ships were close enough to help the stricken boat. The British navy responded, asking for more information, but later said pirates had already boarded the ship and that any sort of naval action would risk harming the crew.
"The British navy instructed us to wait until the pirates contacted us," he said.
Meanwhile, the International Maritime Bureau alerted coalition forces patrolling the region and other military agencies in the area, sending them photos of the vessel, Choong said.
It was unclear if the Indian navy had received the information because it has no direct communication links to the maritime bureau, he said.
"We hope that individual navy warships that are patrolling the gulf would coordinate with the coalition forces or request information from us" to avoid such incidents, Choong added.
It was unclear whether darkness played a role in what happened. The Indian navy said earlier that the final showdown occurred after nightfall.
Somalia, an impoverished nation caught up in an Islamic insurgency, has not had a functioning government since 1991. Somali pirates have become increasingly brazen recently, seizing eight vessels in the past two weeks, including a Saudi supertanker loaded with $100 million worth of crude oil.
There have been 96 pirate attacks this year in Somali waters, with 39 ships hijacked. Fifteen ships with nearly 300 crew are still in the hands of pirates, who have demanded multimillion dollar ransoms.
Shippers worldwide have called for a military blockade of the waters off Somalia's coast to intercept pirate vessels heading out to sea, but NATO officials said there were no such plans.
Associated Press Writers Eileen Ng in Kuala Lumpur and Ambika Ahuja in Bangkok contributed to this report.