The comments come after a rise in attacks against Catholics in recent months.
In January, a pro-government collective interrupted a Mass at a church in Caracas, shouting insults at the priest and preventing the congregation from leaving the building.
Protests also took place outside the home of Archbishop Antonio Lopez Castillo after he spoke out against the government earlier this month.
In a third incident, a group of seminarians were attacked by a group of men, beaten up, and stripped in Merida, in the Venezuelan Andes.
Archbishop Ramon Ovidio Perez Morales told Catholic News Service: "These are not isolated events and sometimes we even ask ourselves to what extent this is a systematic campaign."
The Church appears to have been targeted after it spoke out against alleged human rights abuses by the Venezuelan government.
"This is all part of a general policy of confrontation with the church," said Archbishop Morales. "Specifically, it's against the Venezuelan episcopal conference, and it's nothing new."
Venezuelan bishops and the country's government have had a tense relationship since the election of President Hugo Chavez in 1999.
The Catholic Church had attempted to act as a mediator between political parties last year, but after talks failed, the bishops received some backlash for their failings.
"Clergymen here have said that the principal cause of the country's crisis is that this regime wants to impose a project that is socialist and communist," Archbishop Morales said.
According to the CIA Factbook, 96 per cent of Venezuelans consider themselves Catholic.