Tina Khidasheli, another opposition leader said: "There were about 1,000 police. They started operations at 8am [04:00 GMT].
"They beat us and detained two people as far as I know."
She said police "started a street fight against the demonstrators. They cleaned the street, as they would say".
A Russian television crew said that police seized pictures and video they had filmed during the operation.
The protesters had called for the resignation of Saakashvili accusing him of economic mismanagement and corruption; accusations he refutes.
Gigi Ugulava, Tbilisi's mayor, defended the action by police.
"I was listening to one of the opposition leaders who was saying proudly they planned to pitch tents and set up a tent town in Tbilisi," he told a news briefing.
"What we did is stop this because it is the will of the people not to have a tent town in Tbilisi."
The protest marked the biggest challenge to Saakashvili since his landslide election after the Rose Revolution four years ago.
"Saakashvili has shown strong nerves just for five days, but now we will show him what strong nerves really are," Khidasheli said.
The protesters initially called for changes in the dates of planned elections and in the electoral system, but later made Saakashvili's resignation their central demand.