The scuffles, watched by astonished tourists, erupted when police burst into the grounds of the landmark attraction through a side entrance.
They used tear gas to disperse media covering the event as they tried to corner the protesters and empty the site.
Protesters clung on to the gates, defying repeated orders to clear the entrance.
At least 30 government workers had occupied the Acropolis overnight, barricading themselves inside and changing the padlock on the main gate to keep police out.
Wielding batons and firing two rounds of pepper spray, police pushed protesters away from the entrance and grabbed at least two employees who were whisked off in handcuffs.
A squadron of police officers remained at the gates, allowing tourists free entry to the 2,500 year old monument, Greece’s biggest tourist attraction.
“A prosecutor was called in and orders were issued to clear them out,” Deputy Culture Minister Tylemachos Hytiris told the Athens-based Skai Television network.
Speaking after the operation, one of the leaders of the striking workers, Nikos Hasomeris, said the protests would continue.
“The authorities must accept their responsibilities,” he said. He also accused the authorities of damaging the archaeological site.
Minister Hytiris offered to talk to the protesters but said he could not promise them permanent contracts.
The strike is part of an on-going dispute between the Ministry of Culture and its employees who work at the Acropolis.
Dozens of workers had shut down the Acropolis on Wednesday demanding two years of back-pay.
The protesters said they intended to blockade the Acropolis, Greece’s most famous tourist attraction, until 31 October.
As well as the back-pay issue, the workers are angry that about 320 temporary staff will lose their jobs when their contracts expire at the end of the month. They want the staff to be given permanent contracts.
Sources: BBC, AFP, AP
