Maria del Pilar Hurtado late Friday turned herself over to authorities in Panama, where she fled in 2010.
She was taken on a pre-dawn flight to Bogota, where a judge ordered her to be jailed at the chief prosecutor's office while charges are considered.
Chief prosecutor Eduardo Montealegre said Hurtado was being processed for at least five offences that could bring 15 to 20 years in prison for a conviction.
He said he would urge Hurtado to cooperate and reveal "who gave the order for the illegal wiretapping."
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Hurtado has never implicated the former president in any wrongdoing.
As head of the now-defunct DAS spy agency, she oversaw a scandal-ridden institution whose agents seemed unrestrained in their use of illegal wiretaps to monitor politicians, human rights defenders, journalists and even Supreme Court justices who opposed the former conservative leader.
Dozens of DAS officials, including one of Hurtado's predecessors, have been convicted of illegal spying and providing assistance to right-wing paramilitary death squads. When President Juan Manuel Santos took office in 2010, he immediately disbanded the DAS and pursued charges against several of its former officials.
Her case before Colombia's Supreme Court is among several investigations that Uribe says Santos has launched against some of his former aides.
While serving as Uribe's defence minister, Santos oversaw the military offensive that was credited with bringing down one of the world's highest murder and kidnapping rates.
But the two men are now archenemies, with Uribe accusing Santos of jeopardising security gains in his bid to strike a peace deal with leftist rebels.