Blockades on Antananarivo remain in place
President Didier Ratsiraka had promised to let fuel and other vital commodities through to Antananarivo under a deal signed in Senegal last week.
Disputes over last December's elections have brought much of Madagascar to a halt, as opposition leader Marc Ravalomanana claims he was cheated out of victory.
On Monday, the courts started recounting the votes after the official results had been nullified by the Supreme Court.
Mr Ravalomanana has retracted his declaration that he was president - also under the terms of the Dakar deal.
But governors loyal to Mr Ratsiraka say the people he named as his "ministers" must now also vacate government buildings before they will lift their blockade of the capital.
The BBC's Alastair Leithead says this is a serious blow to the Dakar agreement, which now appears to be falling apart.
Divided island
Mr Ravalomanana enjoys massive support in the capital, where he is mayor.
The governors are based in the eastern port city of Tamatave and bridges on the main road to Antananarivo have been destroyed, leading to shortages in the capital.
If the recount of votes by the High Constitutional Court (HCC) does not give either candidate 50% of the vote, a referendum will be held within six months to decide Madagascar's next leader.
Madagascar has been split in two for several months, with two presidents, two governments, two capitals and splits in the armed forces.
Before the deal was signed, the row had become increasingly violent, with 35 people losing their lives.