Colombia's former intelligence chief has been arrested and charged with murder and collaborating with right-wing militias.
Mr Noguera quit in October but has denied any wrongdoing
Jorge Noguera, head of the Administrative Security Department (DAS), resigned in October but has denied any wrongdoing.
Eight members of President Alvaro Uribe's coalition have been jailed for supporting drug-running militias.
The foreign minister quit this week as her family were investigated for links.
Mr Noguera was arrested after being questioned about supplying the names of unionists and rights workers to right-wing militias.
A number of people on the alleged hit list were murdered.
The investigation has been aided by the testimony of a former Noguera aide, Rafael Garcia, who is serving 18 years for drugs offences, and by information from a laptop linked to a paramilitary leader.
Garcia's lawyer says Mr Noguera is being investigated over the killing of a university professor who was probing the forced displacement of peasants.
The state security agency has been hit by a string of other scandals in the past year, including alleged misappropriation of funds.
Foreign Minister Maria Consuelo Araujo also resigned on Monday pending an investigation into her family links to right-wing paramilitaries.
Mr Uribe was re-elected last year and has been popular for reducing crime.
He has backed a clampdown on leftist militias and overseen the disbanding of thousands of right-wing paramilitaries.
The right-wing militias were formed in the 1980s to fight Marxist guerrillas but both sides have been involved in the cocaine trade.
Tens of thousands of civilians are known to have died in the 40-year conflict between the state and left-wing rebels.