The move came just months after the two countries started to reopen their border following a security dispute.
Colombia's President Juan Manuel Santos said he had complained to his Venezuelan counterpart Nicolas Maduro that Venezuelan troops had been camped out in the Colombian border region of Arauca since Tuesday.
Shortly afterward, Santos said the Venezuelan troops had withdrawn -- but not before triggering a tense row between the two neighbours.
"I told (Maduro) that the situation is totally unacceptable for Colombia," Santos said of his conversation with his Venezuelan counterpart, after meeting with his defence chiefs.
Santos said Colombian "military personnel" had been sent to the area.
"I have instructed the armed forces to stay in the area and continue exercising full sovereignty over the territory."
The foreign ministry said in a statement earlier that it had "information from the Colombian armed forces about the installation of a Venezuelan military camp in the municipality of Arauquita," in Arauca.
It said the government had sent officials to the area to investigate and meet Venezuelan border authorities.
The two countries in August started reopening border crossings after the frontier was closed a year earlier.
That attack was blamed on Colombian paramilitaries, remnants of Colombia's long civil war.
Colombian authorities also reported a further incident in January 2016 in which gunshots were exchanged in the area.
Arauquita is a strategic spot near the two countries' porous border, located on a road linking the Caribbean with the Pacific.
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