Noel Mamere, mayor of Begles, near Bordeaux, officiated at the June 5 marriage between two men - France's first gay wedding - saying he wanted to take a step toward ending discrimination of all kinds.
The order from Interior Minister Dominique de Villepin was based on a law allowing the suspension of mayors who "gravely misunderstand the duties of their office," the ministry said in a statement.
The order was to take effect as soon as Mamere was formally notified.
There was no immediate comment from the politician - well known as a political provocateur - but his lawyer, Caroline Mecary, said she would file two motions, to annul the decision and to suspend its execution.
In France, mayors conduct civil marriages - the only ones with legal weight. However, they do so under the authority of the state prosecutor, the interior minister said.
"The mayor of Begles was, therefore, required to respect the instructions addressed to him by the prosecutor" - to call the marriage off, de Villepin said.
"When he exercises the functions of officer of the civil state, the mayor acts in the name of the state and not of the town," the statement said.
The exchange of vows between Stephane Chapin and Bertrand Charpentier was recorded by television cameras and journalists. Mamere wore the blue, white and red sash of the French Republic when he married the couple.
Prime Minister Jean-Pierre Raffarin and other French authorities had called on Mamere not to officiate at the marriage, saying he would be in breach of the civil code.
On Friday, Mamere denied he had done anything illegal.
"The civil code contains neither a definition of marriage nor a ban on marriage between two people of the same sex," he wrote in a letter to Alain Gehin, prefect of the Gironde region, where Begles is located.
The interior minister said Mamere's case was all the more serious because he "willingly aggravated the fault he committed" by defying the law despite numerous requests that he forego the marriage ceremony and by "giving widespread publicity" to the wedding.
Hours after the marriage, Justice Minister Dominique Perben said that the Bordeaux court would be petitioned to declare the vows null, and de Villepin warned that Mamere would be sanctioned.
Prosecutor Bertrand de Loze has since moved to get the marriage annulled. However, a lawyer for the couple, Remy Giemza, has said he would take the case all the way to the European Court of Human Rights, if need be.
By Emmanuel Georges-Picot