His force had late intelligence about plans to set off rape alarms to distress military horses and throw paint at the procession.
He said: “Officers worked around the clock to try to identify the full criminal network.”
But Sir Mark said it was unfortunate six activists from anti-monarchy group Republic could not go ahead with a peaceful protest.
His force said it regretted their arrest.
Conservative MP Michael Fabricant warned morale among police officers is at “rock bottom” when apologies are issued for them following instructions.
He added: “I’m getting pretty fed up actually with the police apologising all the time.”
Writing in London’s Evening Standard newspaper, Sir Mark defended his under-fire force.
He said: “By Friday evening, only twelve hours from the Coronation, we had become extremely concerned by a rapidly developing intelligence picture suggesting the Coronation could suffer.
“This included people intent on using rape alarms and loud hailers as part of their protest which would have caused distress to military horses.
“We also had intelligence that people intended to extensively vandalise monuments, throw paint at the procession, and incur on to the route.”