Voters will have five days from 20 June to have their signatures checked.
The opposition says the CNE is working in tandem with government to slow down the process.
It blames the government for the country's serious economic crisis.
The petition was handed over to the electoral authorities on 2 May.
The opposition said it had the signatures of 1.85 million voters backing a recall referendum, many more than the 197,000 needed at this initial stage. The CNE said there were 1.97 million signatures.
Mr Maduro's government said there was widespread fraud in the process.
It said the names of thousands of dead voters and children were on the petition, which has been confirmed by CNE President Tibisay Lucena.
More than 600,000 signatures have been invalidated by the electoral bodies.
The other voters who signed the petition will need to have their identities checked between 20 and 24 June.
Opposition leader Henrique Capriles urged voters to get ready to comply with the CNE demand and go to government offices to have their identities checked later this month.
Ms Lucena warned that the process would be immediately suspended until order was restored if there was "any act of violence, trouble or aggression".
Venezuela's National Electoral Council (CNE) has ruled that 1.3 million people who signed a petition for a referendum to oust President Nicolas Maduro will need to turn up at regional electoral offices to confirm their identity.