Some of the Farc fighters who are set to be freed have been held for more than five years in secret jungle camps.
Uribe, in a speech in which he repeated his charges that the fighters kept hostages in conditions worse than those at a concentration camp, said: "We are moving ahead with this unilateral gesture in an effort to free those who today are subject to torture by the Farc."
The government said that the imprisoed Farc members were transferred from 50 prisons nationwide to Chiquinquira jail to the north of Bogota as a first step.
Once freed, the Catholic church and foreign observers will monitor them to see they do not return to fighter bases.
France, Spain and Switzerland are all involved in efforts to broker a deal between the government and the Farc, but so far the two sides have failed to finalise a deal on exchanging jailed rebels for kidnap victims.
Helped by billions of dollars in US aid, Uribe has sent troops to push back the Farc into the jungle, take back areas once under their control and disarm thousands of illegal paramilitaries which had helped fight the Farc.
Details of life in secret fighter hide-outs surfaced last month when a police officer who escaped after nine years in captivity said he was held with Betancourt and the Americans until he fled at the end of April.
He said Betancourt was often chained by her neck to stop her escaping, but that the American men appeared resigned and feared fleeing into the jungles.
The Farc, which began as a peasant army in the 1960s and is now often engaged in Colombia's cocaine trade, wants Uribe to pull back troops from a rural area the size of New York city to facilitate hostage talks.
But Uribe has said that is unacceptable and points to a similar demilitarised zone set up by his predecessor which the Farc used to regroup before peace talks failed.