The ministry said that US-funded Voice of America and Radio Free Europe/Radio Liberty and seven of their media affiliates had been recognised as "carrying out the functions of a foreign agent", in a statement posted on its website.
Those branded "foreign agents" have to present themselves as such on all paperwork and submit to intensive scrutiny of their staffing and financing.
Senators said journalists from outlets labelled as "foreign agents" had been banned from entering Russian parliament's upper house from Tuesday.
On Wednesday, Russian MPs are set to vote on whether to ban those journalists from entering the State Duma lower house of parliament.
Putin last month signed into law hastily issued legislation allowing the measure to target media.
Russia said this was a retaliatory move after Kremlin-backed RT television registered as a "foreign agent" in the United States under official pressure.
Rights groups fear the law could have a chilling effect on the ability of outlets to carry out independent reporting.
Voice of America and Radio Free Europe began broadcasting to the Soviet Union in the 1950s, playing a key role in providing its citizens with uncensored news.
Both broadcasters had already been formally warned by the justice ministry that they risked recognition as "foreign agents."
The justice ministry has now formalised the move, naming them and their affiliates, including Radio Free Europe's news outlets dedicated to Crimea, which Russia annexed from Ukraine, and the Caucasus.
They also include a television channel run jointly by Radio Free Europe and Voice of America called Current Time TV.
Speaking on Current Time TV in Russian, Radio Free Europe/Radio Liberty's president Thomas Kent said that "as a result, the activities of our organisation can face even greater restrictions".
"So far we have no concrete information on these restrictions," the head of the US Congress-funded corporation said.
The 2012 law previously applied only to non-governmental organisations that had international funding.
Many NGOs have closed down as a result, saying the measure made it too difficult for them to operate.
US ambassador to Russia Jon Huntsman said Washington was "very concerned."
"We've seen what this has done to civil society and non-governmental organizations by way of harassment, lawsuits, and effectively putting people out of business," he said in a statement.
"We strongly urge the Russian government not to allow this to stifle free speech and editorial independence on the part of those who seek to operate freely in Russia."
The US State Department said last month that the new law "presents yet another threat to free media in Russia".
It said it was "disingenuous" of Moscow to equate the move to RT's listing as a foreign agent in the US since Washington's measure "does not restrict an organisation's ability to operate".
The head of the Russian upper house's commission for the protection of state sovereignty, Andrei Klimov, said the measure would be strictly enforced but could be reversed.
"If (foreign media) try to get out of it, we will catch up with them anyway, we will force them to obey Russian law," Klimov told Interfax news agency.
"If Washington comes to its senses and ceases pressure on Russian media, however, in that case we will also consider correcting our decisions."
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)