Pollutants in the industrial cities of Krasnoyarsk and Magnitogorsk were found to exceed maximum permissible levels by 30 times, according to the report cited by Kommersant.
Other major contaminated cities include the mining and smelting center Norilsk, which was recently ranked among the 10 most polluted places on earth.
Overall emissions in Russia totaled 31.6 million metric tons last year, representing 1.1-percent growth compared to 2015. Industrial emissions accounted for more than half of that figure, followed by air pollution from vehicles.
The Moscow region leads the country in vehicle emissions, accounting for one-eighth of all pollutants released by vehicles. Kommersant reported in January that vehicles cause up to 80 percent of air pollution in major Russian cities.
The ministry report names the North Caucasus cities of Ingushetia and Kabardino-Balkaria, as well as Sevastopol in Crimea, as Russia’s cleanest cities, but noted growing pollution in all three cities in 2016.