The leaders -- lawyer Felix Agbor Nkongho, teacher Neba Fontem Aforteka'a and Paul Ayah Abine -- were expected to be released soon, one of their lawyers said.
They are among roughly 30 activists being prosecuted on charges that include terrorism as well as rebellion, and which are punishable by death.
Biya's decision, which was announced on state radio, was seen as an effort to calm tensions in the crisis over Anglophone rights in the central African nation of 22 million.
The men were arrested in January after the Anglophone Civil Society Consortium led by Nkongho and Aforteka'a called a strike to promote the rights of the English-speaking minority, which accounts for about 20 percent of the population.
The crisis was triggered by a strike by lawyers demanding that the anglophone regions use Anglo-Saxon common law as their judicial benchmark. Teachers then went on strike.
Biya's decree did not mention by name one of the movement's jailed leaders, the broadcaster Mancho Bibixy, leaving his fate uncertain for the moment.
'Not fundamentally resolve conflict'
Protests in the two main English-speaking regions, in northwest and southwest Cameroon, have pressed for a federal state while some secessionists have even called for independence.
However, the government took a hard line, including the cutting off of internet access for over three months in the two English-speaking regions.
The president's decree also applies to "certain other people detained over the violence in recent months".
"The process of freeing them is under way, but I strongly doubt that it will be tonight,"Claude Assira, a member of the leaders' legal team, said on Wednesday.
Biya's decision came without much warning and as the situation appeared at a stalemate between unyielding authorities and strikes in the anglo areas that have wrought havoc.
"This is a decision that was made to calm the situation, but from my point of view will not fundamentally resolve the conflict," said Mathias Eric Owona Nguini, a politics professor at Yaounde-II University.
"Once the English-speaking leaders are released, will they start agreeing with the regime?" he asked.
The English-speaking minority can be traced back to Cameroon's unique history. At the end of World War II the one-time German colony was handed to France and Britain to run.
The dual communities are a legacy of the unification in 1961 of two colonial-era entities previously run by France and Britain.
An exporter of oil that is rich in timber and agriculture, Cameroon is among the most prosperous economies on the continent.
But the anglophone minority has long complained that wealth has not been shared fairly, and that they have suffered discrimination.
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