But the Indian navy defended its actions, saying it had fired in self-defense.
Noel Choong, who heads the International Maritime Bureau's piracy reporting center in Kuala Lumpur, said one Thai crew member died when the Indian frigate INS Tabar fired on the boat in the Gulf of Aden on Nov. 18.
Fourteen others are missing and a Cambodian sailor was rescued four days later by passing fishermen, he said. The IMB received a report on the apparent mistake late Tuesday from Bangkok-based Sirichai Fisheries, which owned the Ekawat Nava5 vessel, he said.
"The Indian navy assumed it was a pirate vessel because they may have seen armed pirates on board the boat which has been hijacked earlier," Choong said.
India's navy last week said the INS Tabar, which began patrolling the gulf on Nov. 2, battled a pirate "mother vessel" on Nov. 18, setting the ship ablaze.
In New Delhi, Indian navy spokesman Commander Nirad Sinha admitted Wednesday it was possible the ship was hijacked but defended the INS Tabar's action, saying it was responding to pirates' threat to attack it.
"In so far 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 found out about the mishap after speaking to the Cambodian sailor, who is now recuperating in a hospital in Yemen, said Wicharn Sirichaiekawat, the company's managing director. The trawler was headed from Oman to Yemen to deliver fishing equipment when it was hijacked.
"Pirates take over ships," Sinha said. "They've been doing that since the days of Long John Silver."
Choong said the trawler was headed from Oman to Yemen to deliver fishing equipment when it was hijacked, he said.
"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 said.
Sirichaiekawat said his company had contacted the International Maritime Bureau after getting messages from other boats in the region that the Ekawat Nava5 had come under pirate attack. The boat was outfitted with a transmitter sending out its location, which indicated the boat was headed toward the coast of Somalia, he said.
Sirichai Fisheries asked if any naval ships were in the area to help their stricken boat. The British navy responded, asking for information, but later told the company that pirates had already boarded the ship and any sort of attack on them could cause the crew to be harmed.
"The British navy instructed us to wait until the pirates contacted us," he said.
Meanwhile, the International Maritime Bureau alerted the multi-coalition forces patrolling the region and other military agencies in the area, sending them photos of the vessel, Choong said.
However, 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's unclear whether darkness played a role in what happened. The Indian navy said earlier that the final showdown with what they called the "mother ship" happened after nightfall but also said the entire incident had taken a few hours and that it had begun in the evening.
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 so far this year in Somali waters, with 39 ships hijacked. Fifteen ships with nearly 300 crew are still in the hands of pirates, which have demanded multimillion dollar ransom.
At present, warships from Denmark, India, Malaysia, Russia, the U.S. and NATO patrol a vast international maritime corridor, escorting some merchant ships and responding to distress calls in the area.
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. France has also rejected such a call, saying it was not feasible.