Belarus pulled out of high level talks with Russia on Friday due to a dispute over energy prices.
The meeting went ahead anyway, with Russia and Kazakhstan agreeing to launch a customs union on a bilateral basis from 1 July.
Russian Prime Minister Vladimir Putin said he hoped Belarus would still join the union, but that looks unlikely until Moscow and Minsk can reach an agreement over energy prices.
Minsk had initially said it would only join the union if Moscow abolished export duties on oil and gas.
In exchange Belarus offered Russia control of the nation's major energy assets:an offer Moscow rejected on Friday, prompting Belarus' boycott of the customs union.
Moscow says the offer doesn't make financial sense when Russia's state controlled Gazprom already paid a vast amount for a 50 percent stake in Belarus' gas pipeline operator.