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| Player | Team | Goals |
|---|---|---|
| E. Kabaev | Sillamäe Kalev | 36 |
| I. Subbotin | FC Levadia Tallinn | 32 |
| E. Kouadio | FCI Tallinn | 30 |
| A. Prosa | Flora Tallinn | 22 |
| H. Wakui | Kalju Nomme | 21 |
| V. Ivanov | FC Levadia Tallinn | 19 |
| S. Murikhin | Sillamäe Kalev | 16 |
| I. Teever | FC Levadia Tallinn | 15 |
| R. Alliku | Flora Tallinn | 15 |
| T. Neemelo | Kalju Nomme | 14 |
| K. Tiirik | Tammeka | 13 |
| Y. Kvasov | Sillamäe Kalev | 12 |
| D. Ratnikov | Sillamäe Kalev | 10 |
| I. Logua | Flora Tallinn | 10 |
| Z. Beglarishvili | Flora Tallinn | 10 |
| Felipe Nunes | Kalju Nomme | 9 |
| M. Jürgenson | Flora Tallinn | 9 |
| S. Post | Flora Tallinn | 9 |
| V. Plotnikov | Trans Narva | 9 |
| R. Tomson | Paide | 8 |
| L. Omanidze | Tallinna Kalev | 7 |
| N. Mashichev | Sillamäe Kalev | 7 |
| Omar El Hussieny | FC Levadia Tallinn | 7 |
| R. Kirss | Kalju Nomme | 7 |
| A. Nikulin | Lokomotiv | 6 |
| R. Nesterovski | Trans Narva | 6 |
| A. Jõgi | Lokomotiv | 5 |
| A. Škinjov | Trans Narva | 5 |
| D. Kruglov | FC Levadia Tallinn | 5 |
| E. Kharin | FCI Tallinn | 5 |