Roshydrome said two stations in the southern Ural Mountains found "extremely high pollution" of the radioactive isotope between September and October.
Argayash, where pollution levels were 986 times the norm, is located around 20 miles from a huge nuclear reprocessing plant known as Mayak.
The Mayak plant accounts for half of Russian exports of radioactive isotopes although it has denied being the source of increased level of ruthenium 106.
Earlier this month, France's nuclear safety agency earlier this month said that it recorded a spike in radioactivity, and said that "the most plausible zone of release" of this radioactive material "lies between the Volga and the Urals" from a suspected accident involving nuclear fuel or the production of radioactive material.
At the time it said a nuclear reactor could not have been the source of the Ru-106 since other radioactive elements would also have been detected.
After weeks of silence and denials, Russian Federation has confirmed that it too has detected evidence of a mysterious radiation cloud floating above much of Europe, observing a dramatic radiation spike above Russia's Ural Mountains. Mayak was the site of one of the worst nuclear disasters in history in 1957.
Alarmingly high radiation levels nearly 1,000 times above normal levels have been detected in the Ural mountains, according to Russia's meteorological service.
In a statement on Monday, Rosgidromet said the nuclear matter could eventually reach "all European countries starting in Italy and toward the north of Europe".
"The contamination of the atmosphere with ruthenium-106 isotope registered by Rosgidromet is not linked to the activity of Mayak". Ruthenium-106, which is produced by splitting atoms in a reactor, is used in certain medical treatments.
Evgeny Savchenko, the Chelyabinsk region's minister of public security, said that the regional administration had not received any official information about unsafe levels of radiation in September. Today, Mayak is a reprocessing site for spent nuclear fuel.
The Rosatom represtative has stated that there were "no incidents or accidents at nuclear facilities in Russia". It does not occur naturally.
It also demands a check into whether the atmospheric radionuclide monitoring system is sufficiently prepared for possible accidents, and whether public health around a possible release of Ruthenium 106 was sufficiently protected, the environmental pressure group said in a statement. It has prompted demands by Greenpeace's Russian Federation branch for a more "in-depth inquiry".
"Greenpeace will send a letter asking prosecutors to open an inquiry into potential concealment of a nuclear incident", the charity said in a statement.