Prime Minister Vladimir Putin had mentioned plans to impose the ban on Thursday, but denied any link with ongoing political disputes.
His statement came after the U.S. said it might scrap a civil nuclear deal with Russia as punishment for its military action in Georgia and recognition of Georgia's breakaway republics of South Ossetia and Abkhazia.
Rosselkhoznadzor said the decision was a result of a joint Russia-U.S. inspection of poultry firms in late July and early August.
"The inspection also showed that many companies had not taken measures to remove flaws revealed during previous checks," the regulator said in a news release.
Around 120 companies will remain on the list of suppliers to Russia, but the regulator said 29 other firms face the same ban unless they raise their standards.
The United States is Russia's largest poultry supplier. The country has supplied 870,000 metric tons of the 1.2-million-metric-ton poultry quota set by Russia for 2008.
Russia has imposed several temporary bans on pork and poultry from various U.S. producers in recent years. Up to late 2006, the issue was a major stumbling block in bilateral negotiations on Russia's bid to join the World Trade Organization.
The U.S. has strongly criticized Russia's recent actions in Georgia, in the three weeks since Tbilisi tried to seize control of South Ossetia and Russia launched a counterattack.
Moscow has now withdrawn most of its troops from Georgia, and officially recognized South Ossetia and Abkhazia as independent states on Tuesday.
White House spokeswoman Dana Perino said Thursday: "We are in the process of re-evaluating our relationship with Russia, and we are doing that in concert with our international partners."
French Foreign Minister Bernard Kouchner has said European Union leaders are considering sanctions against Russia ahead of a summit on Monday to discuss on the situation in Georgia.