There had been conflicting reports about whether classes held at church would be covered by the new laws.
If passed the proposals would see anywhere offering care to a child for more than six hours a week having to register with Ofsted.
But it had not been clear if Sunday school would be covered by that.
Sir Michael Wilshaw, the head of Ofsted, said they would have to registered so the government "knows they're there".
Speaking to LBC he said: "The government want Sunday schools, madrasas and after-school clubs to be registered. That won't take a lot of time.
"We won't inspect every one of them, but we will know they exist. If there are concerns - if whistle blowers tell us there's an issue - then we will go in."
A consultation on the new laws has closed and they will be debated in parliament next week.
Dr David Landrum, director of advocacy at the Evangelical Alliance, said: "These proposals amount to the state regulation of private religion.
"Sunday schools in churches are publically advertised and in open access buildings. It's also highly unlikely that extremist groups of concern are going to register with the government.
"Sufficient laws already exist in relation to the health and safety and safeguarding of young people. It's misconceived for the government to believe that these proposals will do anything to address the problem it legitimately seeks to solve."