Following his call for a campaign of protest against abortion legislation, the Labour Party called for the religious orders to transfer the rest of the assets promised under the abuse compensation deal.
A Fine Gael minister said the church is entitled to give its views but the Government does not "take orders" from religious orders. And Labour claimed the position on abortion was being misrepresented by the Church.
In his Christmas message, Cardinal Brady urged those who believe in the "fundamental" right to life to lobby TDs.
Transport Minister Leo Varadkar said Cardinal Brady was entitled to give his views.
But a Labour Party TD said he was disappointed by the Cardinal's "misrepresentation" of the legal position and content of the proposed legislation.
In an official statement from Labour, Clare TD Michael McNamara said it appeared Cardinal Brady chooses to "ignore the constitutional position and resultant proposed legislation".
He said the constitutional position was set out clearly by the Supreme Court in the X case.