Hundreds of troops and police commands moved to protesters outside the President's office in Colombo, a few hours before they would leave the area.
A journalist was beaten by the army and a soldier grabbed his phone and deleted the video.
Nine people, including two injured, were arrested by the police.
The police described the incident as "Special Operation to take control of the [return] of the Presidential Secretariat".
When asked about the attack on BBC journalists, a police spokesman said he did not know the incident.
It came when Ranil Wickremesinghe was appointed president on Thursday, after the former President of Gotabaya Rajapaksa fled the country last week.
Separately on Friday, Dinesh Gunawardena - a senior politician who was considered an old loyalist Rajapaksa - took an oath as a new prime minister, stepping to former Wickremesinghe shoes.
Sri Lanka has seen mass riots for months over the economic crisis and many blame the former government for dealing with state finances.
The protest remained peaceful after Wickremesinghe was sworn in at the office on Thursday. Although very disbelief, many demonstrators said they would give him the opportunity to lead the country out of the economic crisis.
In his remarks after his inauguration, he said every effort to overthrow the government or occupy the government buildings was not "not democracy, it violated the law".
On Friday morning, the security forces moved to the protest camp and reclaim the building from the demonstrators, which previously promised to return the building.
The attack occurred in the early hours of Friday, around 01:00 local time (19:30 GMT Thursday). The security forces then fully closed the road to the site.
The tension between the two groups continued to boil in the afternoon because about 100 protesters against the security forces lined up in a line near the President's office.
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