The prisoners were among more than 200 people arrested during clashes with police in May, 2006, in the village of San Salvador Atenco, in central Mexico, in which two civilians died.
The Nobel winners asked President Felipe Calderon to "free the 12 political prisoners, overturn their sentences and cancel their arrest warrants."
It said they had been tortured, held without warrants and sentenced without proof.
They also called for an inquiry into accusations from 50 women that they were raped by police during the operation, which involved some 2,000 officers.
Tensions escalated in Atenco after police attempted to relocate flower vendors from near a market.
Locals resisted, blocked roads and detained 11 police officers.
Mexico's Supreme Court last year ruled that there had been serious rights violations during the Atenco clampdown, but it did not condemn the perpetrators.
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