Former judge Suchinda Yongsunthorn said on Wednesday security forces with heavy weaponry stormed the historic Krue Se mosque and killed Muslim fighters armed only with machetes and a single gun.
The storming of the mosque on 28 April was the final battle of a disastrous uprising that left 108 rebels dead.
It sparked international condemnation amid widespread accusations from the Muslim community that the authorities had been heavy-handed in crushing the unrest - part of a continuing uprising that has seen more than 250 killed this year.
No one blamed
In a report delivered to Prime Minister Thaksin Shinawatra, the six-strong committee did not blame any individual and cleared the military of wrongdoing since martial law had already been imposed across parts of the country's restive south.
But asked if he believed the security forces had used too much force against the lightly armed rebels, Suchinda said: "Yes, I do feel that way.
"Various evidence convinced me, such as the many heavy weapons ... and machine guns used by the military, while the militants had only machetes and one gun with not many stolen bullets," he said.
"The conclusion was neutral, did not point out directly who was to blame and it's merely a direct report of what happened."
"Based on the evidence, we found that the military was authorised in its use of force under martial law but public pressure at the scene also partly fuelled
Suchinda Yongsunthorn, retired Thai judge who headed the
28 April violence inquiry
He added: "Based on the evidence, we found that the military was authorised in its use of force under martial law but public pressure at the scene also partly fuelled the storming."
Gen. Panlop Pinmanee, the military commander who ordered the operation, said he made the right decision to save the lives of his men and to prevent the uprising from spreading.
'Ready to explain'
Three members of the security forces were killed at the mosque and eight injured, General Pinmanee said.
"I had no choice. If I had delayed my decision by two or three hours, there would have been more catastrophe according to surrendered militants, who said they had planned simultaneous attacks in five provinces.
"I am ready to explain my actions to every party concerned, including the prime minister."
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Thaksin set up the inquiry committee - which includes four Muslim members - after coming under fierce international pressure to investigate the killings at the mosque.
The uprising on 28 April also left five members of the security forces dead during fighting in three Muslim-dominated provinces of Pattani, Yala and Narathiwat.
Thailand's south has seen decades of separatist agitation, but after a period of relative peace, trouble flared at the start of this year, with bombings and killings targeting officials, security forces and Buddhist monks.
The violence sparked fears the conflict could broaden into major strife between Muslims, a majority in the south, and the overwhelmingly Buddhist population in Thailand.
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Analysts say Thailand's Muslim-majority south has been largely excluded from the country's recent rapid development, while at the same time Islam has been a growing factor in local politics.
Suchinda said it was down to Thaksin whether or not to make the report public, but warned "heavy-handed" tactics by the government would not solve the problem.
The retired constitutional court judge said the separatist movement, widespread smuggling and the abuse of power by officials appointed by Bangkok, all contributed to the violence.
However, Thaksin's government signalled on Tuesday it was ready to embark on renewed tough military action as killings continued after low-key talks with the rebels.