"I absolutely deny the rumour, published in the Monday April 8th edition of Libération, claiming I have a bank account in Switzerland," Fabius wrote in a statement.
There is no "substance or foundation" to the report, he added.
Fabius also announced that he would pursue legal action to "stop the diffusion of this false and slanderous information".
The headline in Libération read: "A possible Fabius affair petrifies the Elysée", referring to the French president's office.
In the long article there are no facts showing that France's top diplomat has an undeclared foreign bank account, it simply stresses that the Mediapart news website "is exploring this line" of investigation.
Mediapart journalist Fabrice Arfi told Libération that the only news Mediapart had "is what is published on our website".
It was Mediapart that broke the story about former budget minister Jerome Cahuzac having an undeclared bank account in Switzerland.
President Francois Hollande's government has been shaken by the scandal which erupted on Tuesday after Cahuzac – once in charge of tackling tax evasion – admitted to investigators that he had a foreign account containing some €600,000.