The Russian ministry said in a statement that ambassador John Beyrle was quizzed about "recent official statements" from the US State Department and the Moscow embassy concerning the Kuril Islands dispute.
The ministry said that the United States had in those comments "expressed support for Japan's territorial claim against Russia".
"In this connection, the Russian Federation once again laid out it principled and unwavering position on Russia's sovereignty over the south Kurils," the Russian statement said.
But US officials said the entire incident resulted from a misunderstanding in which an old Washington policy line was presented by the Russian media as a recently issued statement.
The decades-old Kuril dispute rose to the top of Moscow's diplomatic agenda with Tokyo in November when President Dmitry Medvedev paid an unexpected visit to one of the four islands at the heart of the dispute.
The two sides have since been engaged in a heated war of words that continued during a tense February 11 exchange in Moscow between Japanese Foreign Minister Seiji Maehara and his Russian counterpart Sergei Lavrov.
A US official, speaking on condition of anonymity, said that a Russian news agency had contacted the US embassy in Moscow shortly after Maehara's visit.
The embassy then dug up an existing State Department position paper on the Kurils stating that Washington encourage dialogue on the dispute while supporting the Japanese claim.
The US official said that Washington's stance on the dispute has not changed since 1952.
Tensions over the Kurils have prevented the signature of a Russian-Japanese peace treaty formally ending World War II hostilities and kept Japanese investments to a minimum in Russia's underdeveloped Far East.
Tokyo says its claim on the islands -- still known as the Northern Territories in Japan -- is backed by the fact that the Soviet Union never signed a 1951 peace treaty formally establishing post-war borders in the Pacific.
But the Kremlin's foreign policy adviser said earlier this month that the islands' status "will not be subject to any review -- either today or tomorrow".
The Russian president has also vowed to modernise the islands' defences and improve their dilapidated infrastructure.