More than 110 people have died since early January in union-led protests against Conte, a reclusive diabetic in his 70s who seized power in an army coup.
"Orders have been given to the heads of the armed forces to take all appropriate measures to defend the people of Guinea from the risk of civil war," Conte said.
Unions resumed the nationwide stoppage because Conte named close ally Eugene Camara as prime minister on Friday.
Union leaders said this violated a power-sharing deal to end an 18-day strike last month which left more than 90 people dead and tested Conte's grip on power.
"We sincerely hope the president will name a prime minister who suits the people," said Boubacar Biro Barry, union negotiator, before Conte's announcement.
Martial law follows violence
The government imposed martial law when the union's protests degenerated into widespread violence on Monday.
Witnesses said at least three people were killed in opposition-controlled suburbs of the capital Conakry on Monday.
In the southeastern town of Nzerekore, local officials reported six protesters killed and dozens injured in clashes with police.
Martial law in Guinea forbids all public meetings and empowers the military to censor newspapers and all radio and television broadcasts.
The army can also monitor private communications, such as telephone calls, faxes and emails.