League table
| Pos | Team | Pld | W | D | L | GF | GA | GD | Pts | Qualification or relegation |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Flora (C) | 28 | 24 | 4 | 0 | 105 | 21 | +84 | 76 | Qualification for Champions League first qualifying round |
| 2 | TVMK | 28 | 20 | 5 | 3 | 82 | 26 | +56 | 65 | Qualification for UEFA Cup first qualifying round[a] |
| 3 | Levadia Maardu[b] | 28 | 15 | 4 | 9 | 54 | 30 | +24 | 49 | |
| 4 | Narva Trans | 28 | 14 | 5 | 9 | 58 | 43 | +15 | 47 | Qualification for Intertoto Cup first round |
| 5 | Tulevik | 28 | 8 | 6 | 14 | 44 | 56 | −12 | 30 | |
| 6 | Levadia Tallinn[c] | 28 | 8 | 4 | 16 | 44 | 63 | −19 | 28 | |
| 7 | Valga | 28 | 3 | 8 | 17 | 25 | 63 | −38 | 17 | Qualification for relegation play-offs |
| 8 | Kuressaare (R) | 28 | 1 | 2 | 25 | 11 | 121 | −110 | 5 | Relegation to Esiliiga |
Source: Estonian Football Association (in Estonian)
Rules for classification: 1) points; 2) number of wins; 3) head-to-head points; 4) head-to-head goal difference; 5) head-to-head goals scored; 6) goal difference; 7) number of goals scored.
(C) Champions; (R) Relegated
Notes:
Rules for classification: 1) points; 2) number of wins; 3) head-to-head points; 4) head-to-head goal difference; 5) head-to-head goals scored; 6) goal difference; 7) number of goals scored.
(C) Champions; (R) Relegated
Notes:
- ^ Levadia Maardu qualified as 2003–04 Estonian Cup winners.
- ^ Levadia Maardu changed their name to Levadia Tallinn in 2004.
- ^ Levadia Tallinn changed their name to Levadia II Tallinn in 2004.
Relegation play-off
| Tervis Pärnu | 2–2 | Valga |
|---|---|---|
Valejev  24'Savotškin 28' |
Raamat 10' Tarassenkov 37' |
| Valga | 3–0 | Tervis Pärnu |
|---|---|---|
| Antonov 33' Tarassenkov 43'Anniste 54' |
Valga won 5–2 on aggregate and retained their Meistriliiga spot for the 2004 season.
