|Top goalscorer||Maksim Gruznov (31)|
FC Levadia won the 2006 Meistriliiga championship and entered the 2007/08 UEFA Champions League 1st Qualifying Round. Narva Trans finished in their best ever silver-medal position, while FC Flora also gained a place compared to last season on 2005 champions FC TVMK's disappointing year. The latter will enter the Intertoto Cup and the other two above mentioned teams enter the UEFA Cup qualifying rounds in the summer of 2007.
The bottom of the table provided some intrigue as well. The two Tartu teams ended mid-table, with Tammeka's youthful-looking squad impressing under experienced coach and ex-international Sergei Ratnikov, in his first year as the head coach. Pärnu Vaprus was perhaps the surprise package of the season finishing seventh on their debut year in the Meistriliiga and bringing Pärnu back on to the Estonian football map. Mainly Russian-speaking Tallinn team, FC Ajax Lasnamäe, proved a point by staying up against all predictions. JK Viljandi Tulevik had a dreadful year and had to go into the play-offs against Esiliiga's JK Tallinna Kalev and lost, which should've meant their relegation a step down. But after the merging of the Tartu clubs, JK Maag and Tammeka, they will still be in the Meistriliiga in 2007. The team with the youngest average aged squad in the league, Warrior Valga, were relegated without a meaningful fight.
The league's top scorers were two JK Narva Trans strikers Maksim Gruznov (with 31 goals) and Dmitri Lipartov (27 goals). FC Flora Tallinn's Vjatšeslav Zahovaiko scored 25, FC Levadia Tallinn's Indrek Zelinski 21 goals.
||Qualification or relegation
|1||Levadia (C)||36||30||4||2||114||29||+85||94||2007–08 UEFA Champions League First qualifying round|
|2||Trans||36||25||8||3||106||36||+70||83||UEFA Cup 2007-08 First qualifying round|
|4||TVMK||36||22||6||8||83||37||+46||72||2007 UEFA Intertoto Cup First round|
|10||Warrior (R)||36||3||2||31||16||110||−94||11||Relegation to 2007 Esiliiga|
Source: Estonian Football Association (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) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round.
Only applicable when the season is not finished:
(Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.
Both games were awarded - / + to Tallinna Kalev since Tulevik fielded an ineligible player.
Kalev had originally won 1 – 1 with away goals
|1||Maksim Gruznov (EST)||Trans Narva||31|
|2||Dmitry Lipartov (RUS)||Trans Narva||27|
|3||Vjatšeslav Zahovaiko (EST)||Flora Tallinn||25|
|4||Indrek Zelinski (EST)||Levadia Tallinn||21|
|5||Aleksandr Dubõkin (EST)||Trans Narva||19|
|6||Vitali Gussev (EST)||Maag Tartu||18|
|–||Vladislav Gussev (EST)||TVMK Tallinn||18|
|–||Konstantin Vassiljev (EST)||Levadia Tallinn||18|
|9||Nikita Andreev (RUS)||Levadia Tallinn||17|
|–||Viktors Dobrecovs (LAT)||TVMK Tallinn||17|
- "Jalgpalliliit tühistas Kalevi ja Tuleviku mängude tulemused". Eesti Päevaleht. 14 November 2006.