"I am more worried about that than where councillors go for their meetings," he said.
The politician described the fears over the location of the new Council as "a side issue".
He told this newspaper: "It will be the new Council body that will decide where the headquarters will be located. What is most important is that further jobs are not allowed to be transferred out of Fermanagh. If councillors have to go to Omagh, I don't care, but I want to ensure that public service jobs are maintained in Enniskillen and that the maximum number of services are delivered from Fermanagh."
Mr Flanagan pointed out that discussions on the Council location have not started yet.
"We are still in very early stage of this amalgamation process," he said.
But according to members of Enniskillen Business Partnership (EBP) who met with local Sinn Fein representatives last week, including Mr Flanagan, the MLA's Council colleagues had a different view.
EBP member Donal McGovern, said: "We were glad to get assurances from Sinn Fein that the councillors will be supporting Enniskillen for the new headquarters for the amalgamated council. They could tell us no benefit to this amalgamation for Fermanagh," he said.
The meeting between Sinn Fein and EBP was in response to rumours that Sinn Fein were instructing its members in both local councils to vote Omagh as the preferred location, something Mr. Flanagan has refuted.
Mr. McGovern added: "I don't think anyone feels we have anything to gain from this amalgamation. Enniskillen and Omagh are two very different towns; Enniskillen and Fermanagh are tourist areas with very different needs than Omagh. We don't have anything against Omagh getting government jobs, as long as Fermanagh does not lose jobs as a result. We don't want to lose any more jobs."
During the meeting, EBP also made it clear to Sinn Fein that businesses here could not sustain any further losses.
"It is a very tough time for people and businesses and I don't think anybody would think it is a time for Councils to spend money at the expense of ratepayers."