Kalev have missed out on a place in the Baltic League after the Estonian Basketball Association selected Ehitustooriist, Tartu Rock, Pirita and Audentes/Nybit as their four representatives in the next campaign.
The league had been told that the top four would qualify for the Baltic League automatically.
However, the national committee appealed for applications and opted to nominate Audentes/Nybit rather than Kalev, who finished third in the league table.
Committee leader Andres Liinat told Estonian daily Eesti Päevaleht: "We have to be honest with our Latvian and Lithuanian colleagues and put out the strongest teams from our country.
"We would like the Estonian national team players to be represented in the participating clubs so that they would get good experience," he added.
"We also had a look at the clubs' results so far and their resources - both human and material."
Liinat also revealed that Kalev's application was unconvincing as their director sent only a short e-mail while other clubs presented thorough application packs.