Lisburn mayor Jim Dillon meeting the Queen last week
The Democratic Unionist Party is accusing Ulster Unionists of doing a deal with Sinn Fein.
However, the UUP has said the move is because of new legislation.
Last week's royal visit was seen as a boost to Lisburn's bid to get city status.
But the DUP said that no sooner had the Queen officially opened the new council offices, than the Union Jack was taken down along with the Queen's portrait.
The portrait is now back in place and councillors have been debating whether to fly the Union flag for just 19 days.
Jonathan Craig of the DUP said Ulster Unionists had done a deal to get Sinn Fein backing for city status.
Equality legislation
"If the price for city status is that the Union Jack is reduced from flying 365 days a year to 19 then the price is far too high," he said.
But Ulster Unionist mayor Jim Dillon said the recommendation was in line with new equality legislation.
"City status never came up. This recommendation would have been debated at this stage, because the last thing this council needs is to end up in a legal situation," he said.
"There is only one set of people who win out of that and that is lawyers."
Sinn Fein said they did not care about city status and they would be arguing against any flying of the Union Jack at next week's full council meeting.
Court decision
Earlier this year, a court dismissed an attempt by Sinn Fein to prevent the flying of the Union Flag on certain days outside public buildings in Northern Ireland.
The case was brought against former Northern Ireland secretary Peter Mandelson on the flying of flags on government buildings.
Sinn Fein mounted the legal challenge to the Flags Order introduced by Mr Mandelson in November 2000 allowing the Union Flag to be flown on 17 designated days.
The party argued that the order was contrary to the spirit of the Good Friday Agreement and discriminated against nationalists.
Designated days include the Queen's Official Birthday and Remembrance Sunday.