| IATA | ICAO | Name | City | Type |
|---|---|---|---|---|
| - | EE-0001 | Aste Air Base | Aste | Closed Airport |
| - | EE-0010 | Kaavi Airfield | Kaavi | Small Airport |
| - | EE-0007 | Kagul Air Base | - | Closed Airport |
| URE | EEKE | Kuressaare Airport | Kuressaare | Medium Airport Scheduled |
| - | EE-0013 | Kuressaare Hospital Helipad | Kuressaare | Heliport |
| - | EEMU | Muhu Airfield | Muhu | Small Airport |
| - | EE-0003 | Nässuma Airstrip | Nässuma | Closed Airport |
| - | EE-0005 | Roomassaare Seaplane Base | Kuressaare | Seaplane Base |
| - | EERU | Ruhnu Airfield | Ringsu | Small Airport Scheduled |
| - | EESE | Salme Heliport | Salme | Heliport |