Speaking at a meeting of the Policing Board on Thursday, Mr Baggott defended the PSNI's initial response to the demonstrations saying their approach had been "measured".
He said: "I will never accept there is any perception that police officers should or will be used as cannon fodder. Any such accusation or perception is wrong.
"When colleagues faced that violence with such commendable courage and restraint they had the authorities to deploy AEP (baton rounds).
You can be assured that AEP's will never be used for crowd control purposes or to concentrate the minds of potential rioters
"In my personal conversations with many colleagues including baton round gunners they have told me they chose not to use those authorities because firstly, they are professional and they saw the need for restraint. I commend them because they saw the bigger picture."
It comes after Police Federation chairman Terry Spence said the policing of the protests, which followed changes to City Hall's flag policy, had been a tactical failure.
Mr Spence said 136 officers were injured and baton rounds should have been used earlier.
"We are not cannon fodder," he commented. "Much of our initial difficulty and injuries can be attributed to us slavishly following the Association of Chief Police Officers' guidelines on tactics to be deployed in the use of baton rounds in public order confrontations.
"To put it bluntly, we were policing public order in NI according to guidelines more appropriate for the rest of the United Kingdom."