"The office is ready for reopening from Monday," a police official told AFP on Sunday, adding that forensics experts had visited the office to gather evidence of damage by protesters.
"The siege of the secretariat, which lasted since 9 May, has now been lifted."
Western governments, the United Nations and human rights groups have condemned Wickremesinghe for using violence against unarmed protesters who had announced their intention to vacate the site later on Friday.
Police spokesman Nihal Talduwa said protesters were free to continue their demonstrations at a designated site near the presidential office.
"They can remain at the official protest site. The government may even open a few more places for demonstrators in the city," Talduwa said Sunday.
The military operation to clear the secretariat building and its immediate surroundings came less than 24 hours after Wickremesinghe was sworn in and just before a new cabinet was appointed.
Wickremesinghe was elected by legislators on Wednesday to replace Rajapaksa, who fled to Singapore and resigned after demonstrators chased him from his palace.