Northern Ireland Health Minister Bairbre de Brun said the problem was one of underfunding.
"If Bairbre de Brun is intent on pursuing this road, then the union will oppose that, " he said.
Sinn Fein MEP Bairbre de Brun welcomed the announcement, saying it "provides the potential for more economic regeneration for cross-border communities".
It was imposed on Mr McGuinness and health minister Bairbre de Brun last year by Northern Ireland First Minister David Trimble.
And the then Northern Ireland health minister Bairbre de Brun indicated there was not enough funding to make the drugs freely available in the province.
Similarly Bairbre De Brun, the province's new health minister, may soon have to modify Sinn Fein's previously blanket opposition to any consideration of hospital and ward closures.
Ulster Unionist leader David Trimble has banned Sinn Fein's Martin McGuinness and Bairbre de Brun from North-South Ministerial Council meetings because of a lack of movement on IRA disarmament.
Democratic Unionist Party members of the Executive have refused to attend meetings of the cabinet due to the presence of Sinn Fein ministers Bairbre de Brun and Martin McGuinness.
The Ardoyne protest was attended by Sinn Fein leader Gerry Adams and his party colleagues Gerry Kelly and Bairbre de Brun, as well as SDLP members including Alex and Tim Attwood.
BBC: NEWS | UK | Northern Ireland | Police praise after parade passes
And Sinn Fein Stormont ministers Martin McGuinness and Bairbre de Brun have written to the first and deputy first ministers calling for an emergency meeting of the executive to discuss the plan.
But in the interim both the Department of Health, run by Bairbre de Brun, and the Department of Education under Martin McGuinness have said they will comply with the regulations and fly the flag.
He also took issue with another part of Mr Trimble's weekend speech - a section which attacked the performance of the Health Minister Bairbre de Brun, and also criticised the Education Minister Martin McGuinness.
Meanwhile, Sinn Fein's Mitchel McLaughlin and Bairbre de Brun will lead a delegation to lobby MPs in London on Thursday ahead of a half-day Westminster debate on the reform of the Royal Ulster Constabulary.
Sinn Fein's two ministers on the Northern Ireland Executive, Martin McGuinness and Bairbre de Brun, might refuse to work in the buildings should the Union flag be flown without the Irish tricolour at its side.
The republicans, representatives of some of the poorest sections of society, will soon face other tests imposed by democratic politics when Bairbre De Brun has to close hospitals and Martin McGuinness cannot end Northern Ireland's selective education system.
应用推荐