Central Workers Union members Jorge Prieto, Leonel Goyeneche and Hector Martinez were all shot dead in the town of Saravena in the province of Arauca on Thursday.
Gloria Florez, director of the human rights group Minga, said on Friday that witnesses saw the men taken from a house by soldiers and "executed extra-judicially".
But the army has denied the allegation.
General Luis Garcia said the three men were meeting with leftist guerrillas from the National Liberaton Army when they were killed during a shootout with soldiers.
Garcia said the three had opened fire on his troops and they were in possession of guns and dynamite.
Union leaders denied the men had links to the guerrillas. Colombian prosecutors are investigating the incident.
According to the Central Workers Union, 574 union members have been killed in Colombia since 2000.