"We captured three Colombian militants and confiscated weapons used by US and Colombian armed forces," Delcy Rodriguez told a news conference.
Interior Minister Carmen Melendez said four national guard and police officers were killed during the operation, dubbed Great Indian Chief Guaicaipuro.
Clashes between security forces and gangs began in the western Caracas neighborhoods on Wednesday night.
Rodriguez said that gang leaders were found to be hoarding food supplies that had been distributed among the poor under the state food security scheme. She said gangs were being financed by the right-wing opposition.
Venezuela launched an operation on 21 March to root out militants in the area near the Venezuelan-Colombian border, destroying several camps, seizing weapons and arresting dozens of people. The operation was initiated in response to an armed attack on a checkpoint controlled by the Venezuelan military in the border city of La Victoria. In early April, eight Venezuelan soldiers were reported to have perished in the clashes, while 34 were injured.