In a live, televised address to the nation, Uribe said a military rescue operation was never authorised.
He also said there were no military operations on June 18, the date the Farc said the attack occurred, in zones where the hostages are thought to have been held.
The president said: "The Farc wants to blame these deaths on the armed forces.
"The Farc wants to hide this crime against humanity that it committed."
Pablo Casas, an analyst with the independent Bogota-based think tank Seguridad & Democracia, said: "It looks like these people died in a random clash with an illegal paramilitary group.
"But there is no doubt that the Farc was responsible for the lives of the people they kidnapped, so the fault remains with them."
Colombia was shocked when the Farc kidnapped the politicians from the provincial capitol building in 2002 by masquerading as soldiers and calmly escorting them onto a bus, saying they were being evacuated due to a bomb scare.
|Farc rebels captured 12 assembly members in a daylight raid in April 2002 [AFP]|
The 12 were among about 60 high-profile hostages, including three American defence contractors and Ingrid Betancourt, a French-Colombian politician whom Uribe wanted to swap for rebels held in government jails.
But Uribe and the Farc have yet to agree on terms for negotiating the hostage exchange.
Betancourt was seized during her 2002 presidential campaign. The Americans were captured the following year while on an anti-drug mission.
Colombia is the world's biggest producer of cocaine. The four-decade-old conflict between Farc and the government has killed thousands of people.
The government blames the Farc for a series of bombs that killed three people, including a three-year-old girl, and injured dozens in the Pacific port city of Buenaventura last weekend.