The policy announcement came four days after conservative evangelist Pat Robertson said Washington should assassinate Chavez, a former soldier who has several times accused the US of plotting to kill him.
The chief of the Justice Ministry's religious affairs unit, Carlos Gonzalez, said on Friday that authorisation of good office permits for missionaries would be curbed while the government tightened regulations on preachers inside Venezuela.
The permits "are suspended for a short time, it could be three or four weeks, while we organise a system to see what additional data we need for people coming into the country to preach", Gonzalez said.
"We were already working on this, but these declarations have made us speed things up," he said.
Robertson later apologised, but his comments have illustrated the political gulf that has opened up between the United States and one of its biggest oil suppliers since Chavez was elected in 1998 promising populist reforms.
The Venezuelan president said on Friday US President George Bush would be to blame if anything happened to him after the comments by Robertson.
"He was expressing the wishes of the US elite... If anything happens to me then the man responsible will be George W Bush. He will be the assassin," Chavez said at a public event. "This is pure terrorism."
Robertson, the founder of the Christian Coalition and a leader of the Christian right that has backed Bush, said that if Chavez "thinks we're trying to assassinate him, I think that we really ought to go ahead and do it".
He retracted his comments on Wednesday, saying he spoke in frustration over Chavez's constant accusations against Washington.
Relations between Caracas and Washington have soured since Chavez survived a brief 2002 coup he says was backed by US authorities. US and Venezuelan officials have since frequently traded accusations.
A close ally of communist Cuba, Chavez presents his self-proclaimed revolution as an alternative to US policies in the region.