Opposition councillors claim the Taoiseach is engaging in a "dirty tricks" campaign, involving the Department of Defence, to scupper the Football Association of Ireland's plans to build a stadium.
The allegations were made following a vote at South Dublin County Council earlier this week to sanction the raising of a height restriction to facilitate the building of a £520 million development in Clondalkin, Co Dublin.
Councillors said a late objection from the Department of Defence concerning height restrictions around Casement Aerodrome, Baldonnel, were designed to have an impact on FAI plans to build Eircom Park in nearby Saggart.
Fine Gael TD Mr Brian Hayes, a member of the county council, said a number of councillors believed the Department was taking instructions from the Department of the Taoiseach.
"There is another agenda going on here in light of the continuing objections to Eircom Park," Mr Hayes said. "I don't know why the Department of Defence has lodged an objection very late in the day; that's why people came up with this conspiracy view about Eircom Park. There is a view that it is part of the fight against the FAI because of a general Government agenda to build a National Stadium. This is totally unproven but it is a view."
However, a spokesman for the Department of Defence said the allegations were "totally untrue".
"We have had no impact from or contact with the Department of the Taoiseach on this. We object practically on a monthly basis to developments that would affect Baldonnel, we didn't just start with Eircom Park."
He said the Department had lodged an objection last December because it would be located within 4 km of Baldonnel and was over 15 metres high. "However if South Dublin County Council decide to grant permission to Eircom Park, so be it. If that happens, the Air Corps will have to change their flight paths and how they do their job."
Labour councillor Mr Don Tipping said it was the feeling of the councillors in his party that there was "politicking going on".
"Bertie Ahern wants the FAI to come on board with regard to the National Stadium. The FAI has its own internal problems which have been well publicised . . . If we hadn't voted the way we did, Eircom Park would have been dead in the water", said Mr Tipping.
Councillors were voting on a material contravention of their development plan, which involved raising the height restriction in the area for the construction of the Wyeth Medica plant. In March, the council had granted permission for the construction but it was necessary for councillors to vote on it.
The Department of Defence, on behalf of the Air Corps, appears to have lodged the objection, which centred on heights of developments north and south of the Naas Road, two weeks ago.
However, councillors voted to accept the Wyeth request and rejected the Department of Defence's call for the other restrictions. The county council will decide later in the year whether to grant planning permission to the FAI for the stadium.