Cork city officials strongly rejected the suggestions.
Cork and Belfast city councils signed the Lagan to the Lee cultural link in Cork City Hall on January 8 during the Cork 2005 opening ceremony.
The project will involve various cultural exchanges between the cities.
The event was attended by President Mary McAleese and Belfast’s Lord Mayor, Alliance Party councillor Tom Ekin.
Yesterday, independent Cork councillor Con O’Connell accused city bosses of hiding the Tricolour and removing the Proclamation from the chamber amid fears they would offend Mr Ekin.
“It was a blatant and gratuitous insult to the people of Cork and to the memory of Terence McSwiney and Tomás MacCurtain,” Mr O’Connell said.
City Hall rejected his claims last night.
The flag was obscured and the Proclamation temporarily removed to allow for the special decoration of the chamber for the event, a council spokesman said. “We have the highest regard for our national flag and national emblems,” he added.
An events company was employed to decorate the chamber. Workers placed a velvet screen around the speaker’s podium to ensure images of Belfast and Cork being displayed on a TV screen would be seen properly. It blocked the Tricolour, the spokesman said.
“All the associated equipment, cables, wires, were behind the velvet screen,” he said.
The spokesman also said the Proclamation was temporarily removed to allow projectors beam images of flowing water symbolising the Lagan and the Lee onto the chamber walls.
Sinn Féin councillor Annette Spillane said she was disappointed.
“I found it very hard to take especially when the President was there. We reported it on the day but it was being televised, and we didn’t want to upset people on the day. But we’ve had no reply to our complaint.”