Four civilians and one policeman died in the violence, and 70 other people were injured, the city's Erawan emergency centre reported in Wednesday
Mr Chalerm said he was sorry about the deaths and injuries inflicted on police and the people.
He was confident the losses were the work of a third party, but could not say clearly whether they were men of a certain colour.
The CMPO director admitted that what happened on Tuesday had affected the morale of the police, who did not have firearms. He said the protesters were armed.
PDRC leader Suthep Thaugsuban was to blame for leading the protesters to Government House despite being fully aware that violence could be a consequence, he said.
Mr Chalerm said that after the Civil Court makes a ruling on the use of the emergency decree this afternoon he would call an urgent meeting of the CMPO to review the operational plan.
He said an alternative plan had been prepared in the event the court ordered the revocation of the emergency decree.
If the decree was annulled, arrest warrants issued under its provisions would also be quashed.
Mr Chalerm said he hoped the court would uphold the decree. He insisted the CMPO had not over-stepped its authority.