Pillay's comments came as Thailand's prime minister, Abhisit Vejajjiva, faced growing questions over his response to the opposition "red shirt" street protests.
A military operation in May to end more than two months of protests left 88 people dead, almost all of them civilians.
The red shirts had been campaigning for Abhisit to resign, saying his government was undemocratic because it came to power in 2008 with army backing after a court ruling threw out the previous administration.
While the protests themselves have ended for the time being, analysts say the issues behind them remain unaddressed, fuelling resentments and driving a damaging a wedge into Thai society.
Thai opposition politicians have accused Abhisit of human rights abuses by ordering the crackdown and parliament has begun debating a no-confidence motion against his government.
Responding to Pillay's call on Monday, Thailand's ambassador in Geneva told the Human Rights Council that an independent commission was being set up "to look into all the incidents that took place during the protests".
"The Thai government deeply regrets the loss of lives and injuries that occurred, and is committed to bringing those responsible to account so as to provide justice to those affected by these tragic incidents," Sihasak Phuangketkeow added.
He said that the use of force to end the protests had been a "last resort" and was in line with international standards.
Sihasak said the Thai government was "open to scrutiny" over its handling of the protests was ready to be subject to legal process.
"The government does not seek to evade any responsibility," he said.