A naval spokesperson said Adm. Surasak Rounroengrom "has insisted that the navy did not kill or shoot at the Rohingya," the Bangkok Post reported Wednesday.
Firing on the Muslim refugees from Myanmar "doesn't even cross our minds," the spokesperson added.
Human Rights Watch has called on the Thai government to investigate claims by Rohingya asylum seekers that Thai sailors fired on them after forcing them onto a boat sent back out to sea.
The incident allegedly occurred Feb. 22 off Phang Nga province.
Prime Minister Yingluck Shinawatra and the foreign ministry both rejected the report.
Yingluck said the government doesn't encourage violence and that she would investigate.
The Thai navy's policy is to feed the Rohingya, put them back on their boat and put the boat back out to sea. Their boat is replaced if it is need of repair. No additional shelter is provided.