| # | Team | Penalty goals |
|---|---|---|
| 1 |  Floriana FC | 5 |
| 2 |  Hamrun Spartans | 5 |
| 3 |  Zabbar St. Patrick | 5 |
| 4 |  Mosta FC | 5 |
| 5 |  Sliema Wanderers | 3 |
| 6 |  Hibernians FC | 3 |
| 7 |  Valletta FC | 3 |
| 8 |  Tarxien Rainbows | 3 |
| 9 |  Gzira United | 3 |
| 10 |  Birkirkara FC | 2 |
| 11 |  Marsaxlokk FC | 2 |
| 12 |  Naxxar Lions | 2 |