An accord with the Vatican gave privileges to the Catholic Church not enjoyed by other churches, he said.
The Venezuelan Episcopal Conference warned this week about growing political polarisation ahead of key legislative elections in September.
Mr Chavez has described local Catholic leaders as "troglodytes".
In a televised speech on Wednesday, President Chavez said he was asking his foreign minister to examine a decades-old agreement with the Vatican.
The accord granted privileges to the Roman Catholic Church that other denominations did not enjoy, he said.
As Venezuela was a secular country, granting privileges to one particular religious group was a violation of the constitution, President Chavez said.
He also challenged the Pope's authority, saying he was the Vatican's head of state but not Christ's emissary on Earth.
"Christ does not need an ambassador. Christ is in the people and in those of us who fight for justice and freedom for the humble," he said.
MarxistPresident Chavez and church leaders have been at odds over the years but in recent weeks the differences have once again come to the fore.
The leader of the Venezuelan Catholic Church, Cardinal Jorge Urosa, has been publicly critical of the Chavez government, most recently decrying the authorities' handling of a corruption scandal over spoiled food.
On 12 July, the Venezuelan bishops' conference expressed concern that "ideological and political polarisation" was creating a hostile environment ahead of the legislative elections on 26 September.
Mr Chavez has accused church leaders, who he has labelled as "troglodytes" and "cavemen", of siding with the opposition.
He said they should stay out of politics and stop trying to instil fear in people by calling him a Marxist.
"I am Marxist, but before Marxist I'm deeply Christian," Mr Chavez said.
SIC: BBC