Uribe's lawyer said on Tuesday his client had asked for asylum at the Costa Rican embassy in the Colombian capital in response to the charges.
More than 60 politicians, many from political parties allied to the president, are under investigation for suspected ties to armed groups.
At least 32 of those are in jail while prosecutors examine their ties to the militias.
Uribe, a former congressional leader, is being sought on charges that he struck deals with former paramilitary commanders, the attorney-general's office said in a statement.
"Uribe is being investigated for a meeting he had with former paramilitary commander Salvatore Mancuso before the elections of March 10, 2002 and with Jairo Castillo Peralta, alias "Pitirri", in November 1998," it said.
Uribe has denied the allegations, describing Castillo as "a liar, an extortionist, a killer and a bandit".
The paramilitaries were initially formed in the 1980s to protect the wealthy from kidnapping and extortion attempts by left-wing rebels, but are believed to have carried out similar activities themselves.
The groups killed thousands of alleged rebel supporters and forced hundreds of thousands from their homes before demobilising in an agreement with Alvaro Uribe's government.
Some jailed paramilitary leaders, including Mancuso, complain their former political allies have unfairly escaped punishment.
The move by prosecutors could fuel concerns among US Democrats who oppose a Colombian trade deal partly because of worries over the paramilitaries influence in politics.