They issued a statement in the south-western province of Toliara threatening "to establish the independent state of Toliara" if the High Constitutional Court, HCC, declared that Marc Ravalomanana won the vote, reports the French news agency, AFP.
On Monday, the HCC began recounting the votes after the Supreme Court had nullified the earlier results because President Ratsiraka had removed several HCC judges as the election began.
The result of the recount will be declared on Monday.
This dispute calls into question a deal signed by Mr Ratsiraka and Mr Ravalomanana in Dakar last week.
Biased
"As a magistrate, I cannot back secessionist moves but if Ravalomanana's camp continues to behave illegally, the independence of the provinces is a risk," Toliara Governor Jean de Dieu Maharante told AFP.
Their declaration was backed by the governors of all the other regions of the Indian Ocean island, except the governor of the capital, Antananarivo, where Mr Ravalomanana has his power-base.
They say that the HCC judges are biased towards Mr Ravalomanana.
"We expected the recount would be done by an independent body with representatives of both parties present and an international adjudicator," said pro-Ratsiraka senator Annick Daahy.
"We the governors of the five autonomous province share the analysis of the Toliara elected officials on this point," Antsiranana Governor Jean-Robert Gara said.
"If Ravalomanana is declared (president) we will reject this foregone conclusion and will be obliged to head towards independence," he said.
Blockade
Mr Ratsiraka's supporters based in the eastern port city of Tamatave have imposed an economic blockade on the capital, Antananarivo, where Mr Ravalomanana has his power base.
This has led to shortages of fuel and other essential commodities.
Under the peace deal signed in Senegal, Mr Ratsiraka promised to dismantle the blockades but the governors have said they will remain in place until Mr Ravalomanana's supporters vacate the government buildings they have occupied.
Mr Ravalomanana has retracted his declaration that he was president - also under the terms of the Dakar deal.
Before the deal was signed, the row had become increasingly violent, with 35 people losing their lives.