Colombia says that Ivan Marquez, a member of FARCs seven member secretariat, is among the rebels hiding in Venezuela.
"The government has evidence showing the presence in Venezuela of leaders of the FARC ... and the terrorist group ELN," a statement from the Colombian government said.
When Colombia issued the statement on Thursday, it claimed proof would be forthcoming. But on Friday, the Colombian government had not provided any evidence.
Venezuela's foreign ministry called the Colombia accusations a "desperate attempt to undermine the ground for an eventual normailsation of bilateral relations" and called Colombia's announcement a "pathetic spectacle".
Two years ago, Colombian forces attacked a Farc camp in neighbouring Ecuador, killing a rebel leader and prompting Ecuador and Venezuela to break off ties with Colombia.
Hugo Chavez, the Venezuelan president, believes Colombia of plotting with the US to attack his country.
Venezuela accused the US embassy in Bogota, Colombia's capital, of "intrigue" for alleged involvement in the statement Colombia released on Thursday.
Juan Manuel Santos recently won presidential elections in Colombia and some analysts hoped his victory would ease tensions with Venezuela.
Prior to the new allegations, Santos invited Chavez to his swearing in ceremony and Chavez said he was considering the invitation.
In its Friday statement, Venezuela's foreign ministry said: "We hope the new government will accept as a top priority the proposal of a Colombia peace plan, which will let all of us in South America usher in a lasting solution to the armed conflict that affects our brother country."