Survivors of the alleged incident on February 22 told Human Rights Watch that sailors opened fire on around 20 Rohingya migrants, killing two of them, as they jumped overboard to escape custody after drifting into Thai waters.
But the incident near a pier in Kuraburi district, southern Phang Nga province, was strenuously denied by Thai officials.
"The Thai navy commander responsible for that area has rejected the report," said foreign ministry spokesman Manasvi Srisodapol, adding there is "no reason to shoot or hurt" Rohingya.
Also refuting the claims, defence ministry spokesman Colonel Thanathip Sawangsang said Thailand acts "on humanitarian principles," providing food and water before allowing the boat people to continue south, towards Malaysia.
The kingdom has faced criticism for pushing Rohingya – who have fled in their thousands since Buddhist-Muslim tensions exploded in their home state of Rakhine in June last year – towards Malaysia or detaining them as illegal immigrants once they are on Thai soil.
In January Thailand was also forced to probe allegations that army officials were involved in the trafficking of Rohingya – who are easy prey for people smugglers demanding large sums of money to transport them to Malaysia.
Those unable to pay are believed to be forced into labour in Thailand.
The Thai government has repeatedly promised to investigate all allegations of human rights violations against the Rohingya.
HRW said the shooting took place as the group of Rohingya jumped from their boat fearing they were about to be detained, prompting the sailors to fire warning shots into the air and then directly into the water.
"Rohingya fleeing Burma (Myanmar) should be given protection, not shot at," said Brad Adams, Asia director at Human Rights Watch.
"The Thai government should urgently investigate why sailors opened fire at boat people helpless in the sea and prosecute all those found responsible."
The UN describe Rohingya as among the most persecuted minority groups in the world. Myanmar views its population of roughly 800,000 Rohingya as illegal Bangladeshi immigrants and denies them citizenship.
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I pity them . If nothing , they can serve as good physical labourers in any nearby country. There is always a dearth of man power and cheap labour. why not use these people for that . That will give them legality and legitimacy.