Street violence over flags is unacceptable and must stop, the Northern Ireland Assembly has warned.
During a special session at Stormont, politicians sent out a strong message to loyalists who rioted and issued death threats in response to the removal of the Union flag from Belfast City Hall.
Mr McGuinness said: "There can be no excuses for the street violence which left 28 police officers injured, Belfast City Council staff injured, drivers of cars and buses intimidated and threatened. There can be no ifs or buts - it must be condemned plain and simple."
The disorder flared after Belfast councillors controversially voted to restrict from 365 to 17 the number of days the Union flag is flown. The riots overshadowed a visit by US secretary of state Hillary Clinton last Friday. Mr McGuinness said the damage done to Belfast's reputation would be difficult to repair.
He said: "As we have done before we must unite so as not to allow those who would wish to drag us back to the past to take advantage of less than clear condemnation of the recent unrest. We must also challenge ourselves to be proactive in the pursuit of mutual respect and recognising that we live in a culturally diverse society."
A motion which unequivocally condemned the rioting and campaign of intimidation, harassment and violent attacks on elected representatives was put forward by the First and Deputy First Ministers. It received cross-party support.
DUP First Minister Peter Robinson said another debate on flying the Union flag over Stormont would start on Tuesday at the Assembly Commission.
Mr Robinson said: "I share the frustration and anger that many people do about the removal of the flag but that frustration and anger should not flow out into violence. We consider it essential that on this day, considering the backdrop against which we are speaking, that this Assembly speaks with one voice. Politics is not about agreeing on everything. But it is about resolving our differences through exclusively peaceful and democratic means."
Up to 28 police officers were injured during the violence, and since Friday night 19 people have been charged with public order offences. PSNI Assistant Chief Constable Will Kerr also said he believed loyalist paramilitaries, including senior figures from the UDA and UVF paramilitaries, had orchestrated the disorder.