He said they were accused of "espionage activity".
Earlier in the day, riot police used tear gas and water cannons to disperse protesters who had massed outside the parliament.
The demonstrators rallied and returned to the scene after police forcibly broke up their protest.
The number of protesters increased rapidly to about 5,000 people and units of black-clad police were deployed after the conventional police force was overwhelmed.
Police carrying truncheons and shields, were seen beating and punching protesters, the AFP news agency reported.
The protests, in their sixth day, mark the biggest challenge to Saakashvili since his landslide election after the Rose Revolution four years ago.
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.
Police did not use truncheons during Wednesday morning's sweep, according to Levan Gachechevadze, an opposition leader, but he said that they had kicked him.
"They beat me, and Saakashvili will be beaten, too," he told the privately owned Imedi television after he returned to the protest.
Amid the continuing unrest, Georgia recalled its ambassador to Russia.
"Georgia's ambassador to Russia, Irakly Chubinishvili, has been recalled to Tbilisi for consultations," Nino Kajaia, a spokeswoman for Georgia's foreign ministry, said on Wednesday.
"The events unfolding in Georgia clearly appear to be linked to Russia."
The protesters had called for the resignation of Saakashvili, accusing him of economic mismanagement and corruption - accusations he rejects.
Speaking of the earlier police operation, Tina Khidasheli, an opposition leader said: "They started operations at 8am [0400 GMT] ... They cleaned the street, as they would say".
Gigi Ugulava, Tbilisi's mayor, defended the action by police, saying: "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.
"What we did is stop this because it is the will of the people not to have a tent town in Tbilisi."