Nazi and Confederate flags at Belfast bonfire site condemned by Robinson and McGuinness.
First Minister Peter Robinson and Deputy First Minister Martin McGuinness added their voices to the widespread condemnation of the flags.
"Nazi flags have nothing to do with unionism," DUP leader Mr Robinson tweeted.
"I commend the residents who removed them. Shameful that such flags were ever erected."
Mr McGuinness posted an image of the Nazi flag on his Twitter account alongside a sinister picture that has emerged in recent days of masked loyalists standing beside graffiti in Belfast threatening Catholics with crucifixion.
"The overwhelming majority of the unionist people will be as disgusted as the rest of us at these displays of hatred," the Sinn Fein chief commented.
The banners, which featured swastikas and SS emblems, appeared on a bonfire at the loyalist Glenfield estate in the Co Antrim seaside town.
A Confederate flag - seen by many as a racist pro-slavery symbol - was also flown in the housing estate.
Mr Dickson said: "This is a deplorable move, particularly coming only days after the debate around the flying of the Confederate flag."
He added it was especially disrespectful when it was flown by those supposedly supporting the Orange Order, which regularly lays wreaths on Remembrance Day in memory of soldiers who fought against Nazi tyranny in World War Two.
"These sorts of actions are not representative of the vast majority of people in Carrick and I know they will join me in utterly condemning it and the evil it stands for," he added.
It's understood that the flags have now been removed from the housing estate following public outrage.
East Antrim MP Sammy Wilson of the DUP said that Nazi flags should have no part in society.
"These flags have absolutely nothing in common with unionism or with loyalism.
"Only a short time ago Carrickfergus played host to part of our Armed Forces Day celebrations and on Sunday the RAF's Red Arrows flew proudly over Carrick Castle.
"People from Northern Ireland fought bravely in our armed forces to defeat the Nazis and these flags should have no part in our society.
"I do not believe that the vast majority of people who will participate in celebrations over the coming weekend want to see such flags flying, and I welcome that they now appear to have been removed."
An Orange Order spokesman denied any connection with flying of the Nazi flags.
"The Orange Institution is not responsible for the erection of these flags in Carrickfergus," he said.
"Such flags are utterly reprehensible and bring shame on loyalist communities.
"They should be removed immediately and consigned to the dustbin of history."
Police said they were "aware of reports of several flags in the Carrickfergus area and are making inquiries".