Loyalists protested outside Belfast's Europa Hotel on Friday where a Sinn Fein conference was taking place.
PSNI Chief Constable Matt Baggott and a number of other senior police officers had to be taken into the hotel through a side door after a small crowd of loyalist protesters gathered at the front of the city centre building.
Up to 20 people held placards which read "PSNI - Gerry Kelly's puppets" and waved Union flags.
Matt Baggott, who was addressing a Sinn Fein-organised event for the first time, used the conference to call for more dialogue around policing.
He warned that the PSNI was being dragged into toxic areas such as parading and the past, and said there should be further discussion on what constitutes public interest.
"We are dragged relentlessly into areas which have become increasingly toxic and are holding us back from protecting people in the here and now that is to do with the past and parades.
"At the moment we are spending huge resources because we are required by law to relentlessly go back into the 70s, 80s and 90s whether that is through inquests or inquiries," said the chief constable.
The chief constable also told the audience his organisation was not perfect, hit back at critics who claimed he had not been impartial during the flag protests and defended what he described as officers' restraint.
"Sometimes we are clumsy in what we do. Sometimes we do not get it right and at the moment we are an organisation in huge transition," added Mr Baggott.
Other invited guests at the Belfast: A City of Equals in an Island of Equals conference were former PUP leader Dawn Purvis, Reverend Harold Good who oversaw the decommissioning of IRA weapons, Pastor Gary Mason from the East Belfast Mission in the loyalist heartland of Newtownards Road and victim's campaigner Alan McBride, whose wife was killed in the Shankill bomb.
During his speech, Mr McGuinness revealed he had secretly met with some of the leaders of the flag protests and claimed politicians had a responsibility to relieve police of the burden of dealing with difficult scenarios.
"During the flag protest I actually met with some of the leaders of the protests. One of them said to me, politically I feel British but culturally I feel Irish.
"Even the comment I am politically British but culturally Irish was common ground that I would stand on with someone that was seen to be in the leadership of the flag protests. I think solutions to all of these big challenges can be found," he said.
Mr McGuinness said he would love to attend events in loyalist heartlands such as the Shankill Road or Portadown but invitations were few and far between.
He also defended his decision to meet and shake hands with the Queen during her visit to Belfast last year.
Meanwhile, the Sinn Fein deputy leader extended good wishes to Prince Philip who has been taken to hospital.
"Even this morning we hear that Prince Philip has been taken to hospital and will be there for the next number of weeks and obviously we wish them well," he said.