It is the first major social network to be blocked by Russian authorities.
It said that the order came to ensure the company complied with a court ruling that found it guilty of violating data laws.
Roskomnadzor, the watchdog, said it was acting to protect Russian Internet users’ data.
Russian law requires websites which store the personal data of Russian citizens to do so on Russian servers, something it said LinkedIn did not do.
LinkedIn, headquartered in the U.S., has over six million registered users in Russia.
It is the first major social network to be blocked by Russian authorities, setting a precedent for the way foreign Internet firms operate.
Roskomnadzor spokesman Vadim Ampelonsky said that LinkedIn’s site would become unavailable in Russia within a day.
One Internet service provider, Rostelcom, was quick to say it had already blocked access to the site.
However LinkedIn could not be immediately reached for comment.
It said in a statement earlier this month that the decision risked denying access to its site for millions of Russian members, including companies, who use it to grow their businesses.
The law requiring websites which store the personal data of Russian citizens to do so on Russian servers was introduced in 2014, but never previously enforced.
Critics see the move against LinkedIn as part of an attack on social networks in a country which has increasingly tightened control over the Internet in recent years.