The clash comes against a backdrop of growing public protests against the kingdom's long-ruling Prime Minister Hun Sen.
Police fired warning shots in the air and then fired at the protesters, leaving at least three people injured, according to an AFP photographer.
It is the latest in a series of violent clashes between security forces and textile workers demanding higher wages.
The incident happened after thousands of workers blocked the road in front of factories and later faced off with security personnel in the Veng Sreng area of Phnom Penh.
Security forces "used rifles and other things to crack down on the strikers," he said. "They beat them on their heads."
Military police spokesman Kheng Tito said the crackdown came after nine policemen were injured by stones and slingshots.
He said two protesters were arrested.
"We were afraid about the security so we had to crack down on them," said Kheng Tito.
"If we allow them to continue the strike it will become anarchy."
The clash came a day after a special military unit was deployed against garment workers, leaving several injured in a move described by rights activists as a "disturbing new tactic" by the authorities.
The sector employs about 650,000 people and is a key source of foreign income for the impoverished country.
The workers are demanding a minimum wage of $160 per month.
Recently striking garment workers have teamed up with anti-government protesters demanding Hun Sen step down and call a new election because of alleged vote fraud.
There have been daily rallies in Phnom Penh against Hun Sen's government, with an estimated 20,000 or more opposition supporters taking to the streets on Sunday.
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