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.
The banning 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.
They 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 include the right to stop people travelling out of the country if they are suspected of trying to join jihadist groups.
France's law allows authorities to block websites that call for or glamorize terrorism. This law against condoning crime and inciting terrorism was introduced in France after January's terror attacks left 17 dead.
Interior Minister Bernard Cazeneuve visited the US last month, meeting with heads of major online companies like Facebook and Google in an attempt to prevent "the great area of freedom and growth" from becoming a "space of fanatic indoctrination."