One of the sites — al-Hayat Media Center — is accused of links to the Islamic State group, the ministry said.
The site “islamic-news.info” has also been blocked since the end of last week.
“I do not want to see sites that could lead people to take up arms on the Internet,” Interior Minister Bernard Cazeneuve said.
“I make a distinction between freedom of expression and the spread of messages that serve to glorify terrorism. These hate messages are a crime.”
The ban order was given to Internet service providers, who had 24 hours to take “all necessary measures to block the listing of these addresses” under the new rules.
An interior ministry official acknowledged that a ban on the host or publisher sites, which remain unidentified, would have been more effective than Internet providers receiving blocking orders.
“We are in an evaluation and trial phase,” he said.
Despite this flaw, the ministry said that similar operations would target “dozens” of other sites.
The new rules were introduced as part of a package of counter-terrorism measures approved by parliament in November.
Critics argued they could breach citizens’ rights by bypassing the need for a judge to make the banning orders.
Other powers of the counter-terrorism measures include the right to stop people travelling out of the country if they are suspected of trying to join jihadist groups.
Six French citizens aged between 23 and 28 had their passports and identity cards confiscated in February for a period of six months. The order can be renewed.
Cazeneuve said at the time that 40 more people were likely to be barred from travelling in the coming weeks.
He visited California last month, meeting major Internet firms in a bid to improve information-sharing about online jihadist networks, and was due to meet Internet company bosses again in Paris in early April.
The interior ministry has set up a warning system through which friends and family can alert authorities about potential jihadist cases.
Cazeneuve said last month that the ministry had been alerted to over 1,000 cases and that “several dozen” planned trips to Syria and Iraq had been prevented as a result.
Some 1,400 people living in France have either joined the jihadist cause in Syria and Iraq or are planning to do so, Prime Minister Manuel Valls said in March-AFP