The governor of the northern province of La Guajira was arrested by Colombian Attorney General's Office agents on murder and criminal conspiracy charges, officials said.
Jose Francisco Gomez Cerchar was arrested Saturday on a warrant issued by prosecutor Martha Lucia Zamora.
Gomez, known as "Kiko," is being investigated for allegedly having links to paramilitary groups.
The governor has been linked to the 1997 murder of Barrancas city councilman Luis Lopez Peralta and the killings in 2000 of Luis Alejandro Rodriguez Frias and Rosa Mercedes Cabrera Alfaro, Deputy Attorney General Jorge Perdomo said.
Investigators have also linked Gomez to militia chief Rodrigo Tovar Pupo, known as "Jorge 40," and other paramilitary groups.
Tovar Pupo was one of the top leaders of the United Self-Defense Forces of Colombia, or AUC.
Gomez was arrested in his hometown of Barrancas, where he was attending a festival.
The governor took refuge in his house, which was surrounded by his supporters as AG's office agents arrived to arrest him.
Gomez, who served as mayor of Barrancas from 1995 to 1997 and again from 2001 to 2003, was elected governor of La Guajira in 2011.
The AUC, accused of committing numerous human rights violations, demobilized more than 31,000 of its fighters between the end of 2003 and mid-2006 as part of the peace process with former President Alvaro Uribe's administration.
The group was made up of numerous rural defense cooperatives formed more than 25 years ago to battle leftist rebels.
Many of the militias, however, degenerated into death squads and carried out massacres of peasants suspected of having rebel sympathies, along with slayings of journalists and union members accused of favoring the leftist insurgents.
On May 13, 2008, the Colombian government extradited 14 former AUC chiefs, including Tovar Pupo, to the United States.
The former AUC commanders were wanted in the United States on drug, money laundering and other charges. EFE