Miguel Maza Marquez was the director of the now-defunct Administrative Security Department (DAS) when Galan, the leading candidate for the 1990 presidential vote, was gunned down in front of thousands of people at a campaign rally on August 18, 1989.
Prosecutors accuse the ex-spy chief of helping plot the assassination and assigning an "unfit" agent to head Galan's security detail.
Galan's security chief is believed to have had "links to the criminal groups that planned and carried out the homicide," the charge sheet says.
Galan, a senator who was running on the Liberal party ticket, had vowed to extradite drug kingpins like Pablo Escobar, the powerful head of the Medellin cartel, to the United States.
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Escobar's top hitman, John Jairo "Popeye" Velazquez, was convicted of the killing. Liberal politician Alberto Santofimio, a rival of Galan, was later convicted of orchestrating it.
Galan was one of four presidential candidates killed in the bloody run-up to the 1990 election, as Colombia's powerful drug lords waged war on a political movement to extradite them to the United States.
Escobar was ultimately killed in a rooftop gunfight with police in Medellin in 1993.