The Minister for Justice, Mr McDowell, could face a lengthy battle to save his holiday home overlooking the Shannon.
The Minister will hope no one objects to his application to retain the multi-level house at Lavagh, Roosky, Co Roscommon.
Builders burrowed down 7 ft deeper than they were entitled to under the permission granted in 1999. The planners also have a query about the finish on the building. The permission allows for a "thick stone or rendered blockwork" finish, but the official view is that the finish now on the house is different.
Mr McDowell said on RTÉ yesterday that he had engaged "two responsible companies to build a house in conformity with the planning permission" which Roscommon County Council had granted.
"I'm quite happy to abide by the views of the experts in this matter. Nobody's above the law or beneath the law and I, like everybody else in our society, every other citizen, have to obey the law."
The first he knew of the difficulties was when he was contacted by Sky News Ireland on Monday.
Mr John Tiernan, the Roscommon county manager, said yesterday that Mr McDowell and his wife, Prof Niamh Brennan, would have to apply for the house to be retained.
"Due to the fact that the house, which is now substantially complete, is different in external finish and in relation to floor levels, that are some two metres lower than those originally permitted, the planning authority deemed that an extension of time could not be granted and wrote to the agent to advise the client that an application for retention of the dwelling under construction should be submitted, as is the normal procedure in circumstances such as this," Mr Tiernan said in a prepared statement.
There were no objections to the house when the original planning permission was sought in 1999 but objectors could emerge now that the house has been built to a different specification.
The house, which is on a one-acre site by Lake Carrandoe, features a penthouse master bedroom on the fourth floor with uninterrupted views of the River Shannon. A gallery adjoins the master bedroom. There are three other en-suite bedrooms, a study, kitchen, dining-room, living room, laundry and conservatory.
Mr McDowell was forced back into the planning process because he did not complete the house by the end of August this year, the date when planning permission expired.
This meant he had to apply to Roscommon County Council for an extension on August 13th. His project team, Jennings O'Donovan and Partners, undertook that work would be completed by the end of November.
However, council planners ruled on October 5th that an extension should not be granted.
"The question of extension to the duration of the permission does not arise, as the dwelling under construction does not have the benefit of planning permission," wrote Mr John Cunningham, director of services, in an internal council memorandum on the McDowell file in Roscommon County Council's planning section.
Mr Cunningham also said the house built was "significantly different" to that for which permission was granted.
There were no workers at the house yesterday and the site was locked up with safety warnings.