Among the best known channels shut down is CNB, which airs in Caracas and nearby Valencia, and is part of a national network that has been critical of the Venezuelan president.
Last month Conatel launched a survey of radio broadcasters, asking them to present documentation showing the validity of their licences.
More than 200 stations are still under investigation for failing to update their registrations.
Al Jazeera's Dima Khatib, reporting from the capital, Caracas, said: "It looks like a legal measurement but although it does comply with all kinds of regulations... it looks like the opposition is the most affected because the opposition does control most of the private radio stations."
"This is a very polarised society with very polarised media. You have the government media that shows you a perfect Venezuela where everyone is happy, and the opposition media shows you a very bad Venezuela where no-one is happy."
The Venezuelan Chamber of Radio Broadcasters described the closures as a "enormous violation".
The decision came amid government efforts to formulate a new media law, setting out prison sentences for "media crimes".
Human Rights Watch has said the proposed law would "reduce the ability of government critics to voice their opinions and will seriously limit freedom of expression in Venezuela."
Meanwhile, the Venezuelan parliamentarians on Friday approved an election law to redraw voting districts, a step that opponents of Chavez say will give his party a big advantage in next year's congressional vote.
The law also changes Venezuela's proportional representation system in a
way that will likely hurt smaller parties.
The bill easily passed the national assembly, which is dominated by Chavez