The six detainees have been identified as Andres M, Jose N, Eddy G, Camilo R, Jules C, and Jhon Rodriguez, Mr Zapata told a press conference on Thursday.
He added that during the police raid that resulted in their arrest, officers found a rifle, a submachine gun, four pistols, three grenades, four boxes of ammunition, two motorbikes, and a vehicle that had been reported stolen in the group’s possession.
A vocal critic of organized crime, Mr Villavicencio was one of the few presidential candidates to allege links between corruption and government officials.
Mr Villavicencio, a member of the country’s national assembly, had received threats from a gang calling itself Los Choneros last month and had been given a security detail.
He was one of eight candidates in the running for the first round of the election with a focus on fighting corruption - and he and his team had been threatened by the leader of a gang linked to drug-trafficking.
Once a relatively peaceful nation, Ecuador has been ravaged by the arrival of international drug cartels profiting from a boom in cocaine trafficking - and the issue can only grow in importance in the presidential election campaign.