Thai maritime police said they opened fire on a Vietnamese fishing boat while trying to intercept another vessel in waters near Malaysia last week, a clash Vietnamese state media said killed a fisherman and wounded two others.
Officials from the two countries were quoted on Wednesday giving starkly different accounts of the incident and Vietnamese Communist Party media said it could eventually be addressed at the diplomatic level.
Vietnamese fishing boats, which number an estimated 128,000, have repeatedly clashed with Chinese vessels in the disputed South China Sea, but incidents involving Thai boats are infrequent.
Thai maritime police chief, Maj Gen Grittapol Yeesakhorn, said he was unaware of casualties and police were only protecting themselves when their boat was surrounded by hostile Vietnamese vessels trying to ram their boat on Friday.
Police said a Thai officer was aboard a Vietnamese trawler that was stranded with engine trouble before the other Vietnamese boats arrived in support in the incident 40km off the southernmost Thai province of Narathiwat, near Malaysia.
"We had no intention of killing anyone. We fired only warning shots, from 100 metres away. We only shot at the front of the boat," he told Reuters by phone.
"The Vietnamese fishing boat came into Thai waters illegally, police had to arrest them."
Meanwhile, Vietnam's Communist Party-run Nhan Dan online newspaper said hostile incidents took place in overlapping maritime territory between Malaysia, Vietnam and Thailand.
Vietnamese state-run VTV showed footage of injured Vietnamese fishermen being treated in hospital.
Citing the border guard force of Vietnam's coastal Kien Giang province, Nhan Dan said Vietnamese vessels fled as a Thai police boat approached, blaring through a radio: "Vietnam vessel stop, if not we will shoot you to death."
Nhan Dan said Thai police gave chase on three separate occasions and those shot were on different boats. One boat was boarded by police, who tied up the crew and stole a gun and equipment.
One captain was shot dead, at which point Thai police released all crew and left the area, it said.
The Vietnamese probe concluded Thai police "were in violation of Vietnamese and international laws", and proposed the issue be addressed at a diplomatic level, Nhan Dan said.