The ministry named the outlets as the U.S. Congress-funded Radio Free Europe/Radio Liberty and seven of its affiliates, and Voice of America.
Russia's justice ministry said in a statement on its website on Tuesday it had now formally designated US government-sponsored VOA and RFE/RL, along with seven separate Russian or local-language news outlets run by RFE/RL, as "fulfilling the role of foreign agents".
The list also includes the Kavkaz.Realii, Krym Realii and Sibir Realii websites, the Current Time TV channel - a joint project of Voice of America and Radio Free Europe / Radio Liberty - the Radio Liberty-owned factograph.info website and IdelRealii project.
Speaking to Russia's news agency Interfax, senior Federation Council member Andrey Klimov said that labeling the nine outlets as foreign agents might still be revoked.
A vote on the measures is expected next week.
Congress has also revoked the accreditation of RT, prompting the Russian lower house of parliament, the State Duma, to consider a ban of USA media.
US intelligence agencies have alleged that RT served as a tool for the Kremlin to meddle in the 2016 USA presidential election. Russian lawmakers rushed through the necessary legislation last month and President Vladimir Putin signed off on it on November 25.
The legislation has been condemned by rights groups including Reporters Without Borders, which called the legislation an "eye-for-eye response" that would seriously damage media freedoms.
Russian sources, including Mr Klimov who spoke to Russia Today, insisted that the list announced on Tuesday would not be expanded.
In the USA, a committee governing Capitol Hill access for broadcast journalists withdrew credentials for Russia's state-funded RT television after it complied with a US demand that it register as a foreign agent.
"This is very vague and it really opens the way to broad application", he said.
In a video statement, Radio Free Europe/Radio Liberty President Tom Kent said it was unclear how the organisation would be affected by the moves and that it would "study carefully" communications from Russian Federation. "We remain committed to accurate and comprehensive journalism".