"We all know that the current Pope is characterized as a conservative man, but that doesn't necessarily mean that we must automatically think that any word he utters ... is against Venezuela," Information Minister Willian Lara told state television.
Pope Benedict XVI concluded a trip to neighboring Brazil on Sunday by telling a bishop's conference that Marxism - as well as unchecked capitalism and globalization - were to blame for many of the region's problems.
"The Marxist system, where it found its way into government, not only left a sad heritage of economic and ecological destruction, but also a painful destruction of the human spirit," the pope said.
Chavez has explicitly embraced Marxism and is a close ally of communist Cuba. Left-leaning leaders also govern in Bolivia, Eduador, Nicaragua, Chile, Brazil, Argentina and Uruguay, though most do not claim to be Marxist.
Marxism also still influences some Catholic activists in Latin America, remnants of the liberation theology movement Benedict moved to crush as a cardinal. Liberation theology holds that faith should help free the oppressed.
Chavez also says he is a Catholic and calls Jesus an exemplary revolutionary. But he has repeatedly clashed with Venezuelan church leaders since his election in 1998.
Cardinal Jorge Urosa Savino recently criticized the government's decision not to renew the broadcast license of opposition-sided TV channel RCTV. Other priests have warned of increasing authoritarianism under Chavez.
Most Venezuelans are Roman Catholic and the church wields tremendous influence among parishioners.