| # | Team | Penalty goals |
|---|---|---|
| 1 |  FK Yenisey Krasnoyarsk | 6 |
| 2 |  Spartak Kostroma | 6 |
| 3 |  FC Kamaz Naberezhnye Chelny | 5 |
| 4 |  FC Ska-Khabarovsk | 5 |
| 5 |  FK Chelyabinsk | 5 |
| 6 |  Rodina Moskva | 4 |
| 7 |  Arsenal Tula | 4 |
| 8 |  Chernomorets Novorossijsk | 4 |
| 9 |  Chaika Peschanokopskoe | 3 |
| 10 |  FC Rotor Volgograd | 3 |
| 11 |  FK Ufa | 2 |
| 12 |  Fakel Voronezh | 2 |
| 13 |  Neftekhimik | 2 |
| 14 |  Torpedo Moscow | 2 |
| 15 |  FC Ural Yekaterinburg | 1 |
| 16 |  Volga Ulyanovsk | 1 |
| 17 |  Sokol Saratov | 1 |