Social media posts showed officers dressed in riot gear pulling down protest tents and arresting demonstrators outside the presidential offices at Galle Face, two days after the crisis-hit country swore in a new leader.
Police Spokesperson SSP Nihal Thalduwa confirmed nine men were arrested and will appear in court on Friday.
On Friday, Wickremesinghe swore in Dinesh Gunawardena, another Rajapaksa ally, as prime minister. Wickremesinghe and Gunawardena were classmates at Colombo's elite Royal College.
A CNN team in the capital confirmed the situation on the streets was calm following the morning raid, but a heavy military and police presence remained in and around the main protest site.
All roads and lanes leading to the area had been cordoned off and were manned by security forces.
Armed forces now guard the entrance to the Presidential Secretariat and appear to have full control of the building. Banners that were hung from top of the secretariat have also been removed.
Some observers have raised concerns about the level of force used in the raid.
The Bar Association of Sri Lanka also said in a statement that it "strongly and unreservedly" condemns "the use of force and violence" by the authorities "in attacking protesters."
The Human Rights Commission of Sri Lanka also condemned the raid, calling it a "brutal and despicable attack on peaceful protesters" and a "total violation of the fundamental rights of the people."
US and British diplomats also expressed concern.