The UN's human rights agency has urged Thailand to carry out an urgent investigation into Wednesday's clashes.
The mood was reported to be one of sadness and anger
The agency's acting head, Bertrand Ramcharan, said the investigation should be "swift and transparent".
More than 100 youths were killed by security forces, after they carried out a series of raids on police and army posts in three southern provinces.
The government has defended the killings, saying security forces had to take "strong and decisive action".
The Thai Foreign Ministry said in a statement: "The death toll is indeed unfortunate. But given the scale and intensity and swiftness of the attacks carried out by the militants, the government had to take strong and decisive action."
But Mr Ramcharan reminded the Thai security forces of their obligations under international law, to refrain from excessive force.
"He urged immediate measures be taken to ensure full respect for
the human rights of all concerned, including those detained
following Wednesday's confrontations," said UN spokesman Jose Diaz.
The UN is not alone in questioning the level of force used by the Thai security forces to quash the attacks.
The New York-based group Human Rights Watch said on Thursday that Thailand should investigate whether "such a high level of lethal force was necessary", and Muslim leaders have also questioned the severity of the authorities' response.
The worst fighting took place at the Krue-Sae mosque in Pattani province, where 32 people were killed.
Police said Mama Matiyoh told them he was willing to die for Allah
On Friday, mourners gathered at the mosque to pay their respects to the dead. The mood was reported to be a mix of sadness and anger.
"The military could have caught them without killing them, but they didn't," one man told the French news agency AFP.
According to the Foreign Ministry statement, the clash at the mosque "threatened to escalate, compelling the security forces to take decisive actions to bring the situation under control".
The Foreign Ministry statement reiterated Prime Minister Thaksin
Shinawatra's assertion that Wednesday's violence had no connection
with international terrorism or "sectarian and
But there is mounting evidence to the contrary.
On Friday, senior security adviser Gen Kitti Rattanchaya said the attackers had been trained both in Thailand and overseas, and were ready to sacrifice themselves.
Mama Matiyoh, whom police accuse of taking part in an attack in Yala, said he and his colleagues were willing to die for Allah, according to the Bangkok Post newspaper.
He reportedly said they took part in the uprising because they wanted to declare an Islamic state in the south of Thailand.
A statement purporting to be from the local separatist group Pulo (Patani United Liberation Organisation) urged the Malay people in southern Thailand and Muslims throughout the country to follow Islamic teachings.
The statement, which appeared on Pulo's website on Friday, warned Muslims not to go to venues such as bars, nightclubs and concerts, asking them instead to stay at home or in mosques.
"If you follow this instruction you will live in happiness," the statement said.