The alleged spying was revealed Tuesday by the weekly Semana, prompting the firing of two military intelligence chiefs.
Among those allegedly spied on was President Juan Manuel Santos' negotiating team at peace talks with the FARC in Havana.
In ordering a probe, Santos said "dark forces" were trying to sabotage the peace talks, but was not more specific.
However, the FARC's chief negotiator at the talks, Ivan Marquez, yesterday pointed the finger at Uribe, a hardliner who has bitterly opposed the peace talks.
"Don't forget Alvaro Uribe Velez is public enemy number one of peace in Colombia," he said.
Marquez said the spying also targeted the FARC's delegation to the talks, and said the government should explain.
In Bogota, Santos said he had given the army's inspector general ten days to complete his investigation. Colombia's attorney general office is conducting a separate probe.
"This is an investigation that should not be hard to carry out because what they need to show is whether the intel work (the military) was doing was normal intel, which should be protected, or if they engaged in illegal intelligence gathering," Santos explained.
Ivan Cepeda, a congressional candidate for the leftist Alternative Democratic Pole, told AFP the threats were part of "a campaign to destabilize the country and sow unrest to sabotage the peace process in Havana."
Since November 2012, the Colombian government has been in negotiations with the FARC, the country's largest and longest-fighting insurgency. It has been at arms since 1964.
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