The department for local government denied that it is impeding the St Paul's Bay, Kirkop and Msida local councils.
Last week, Labour MP Stefan Buontempo said the Nationalist government discriminated against Labour-led local councils.
He said it is clear that the GonziPN government is hindering the work of certain local councils such as the councils in St Paul's Bay, Kirkop and Msida, which are all led by Labour majorities.
Buontempo explained that due to this discrimination the councils "cannot carry out their duties."
The MP pointed out that the government is dragging its feet in appointing executive secretaries and stopping councils from implementing their programmes.
In a statement issued today, the department said "It is a pity that Stefan Buontempo tried to blemish the department by twisting the facts."
The department said that in all three cases, the executive secretaries chose to work for other local councils according to established procedures.
It explained that the selection process for the new executive secretaries for the St Paul's Bay and Kirkop councils is close to being finalized and added that in the meantime agent secretaries have been appointed to fill the void.
The department pointed out that it has received no complaints from the Kirkop local council about the situation.
As for the Msida local council, the department explained that the current executive secretary will soon move to the Sliema local council.
It added that in the meantime, the Msida council has re-issued a call for applications since nobody was selected following the original call. The department noted that an agent secretary will soon be appointed once the outgoing secretary vacates the post.
The department for local government, which falls under the remit of the Office of the Prime Minister also explained that executive secretaries are selected by an ad hoc board set up by the local council in question.
It added that in the absence of an agreement, the department appoints an agent secretary in conjunction with the mayor.