"I can't see any kind of justification" for the 90-day suspension, Santos Silva said.
Venezuelan authorities took the step Monday after TAP last week carried opposition leader Juan Guaidó and his uncle home from an international tour aimed at ousting President Nicolás Maduro.
Guaidó's uncle was arrested upon landing and accused of trying to bring a small amount of explosives into Venezuela. Portugal ordered an official investigation into that allegation, and Santos Silva said it hasn't finished yet.
The suspension is a "hostile act" against Portugal, Santos Silva told national news agency Lusa, in comments published by online newspaper Observador.
Portugal is in a coalition of European and Latin American nations, called the "International Contact Group," that has backed Guaidó against Maduro. Thousands of Portuguese immigrants live in Venezuela.
Santos Silva said the suspension would also hurt Venezuelans because the Portuguese flag carrier is one of the few international airlines still serving Caracas, with twice weekly flights.
TAP said in a statement it "meets all the legal and safety requirements demanded" by authorities in both Portugal and Venezuela.