Russia will resume accession talks, now in their sixteenth year, next month, and it could possibly join the WTO within a year amid generally better ties with Brussels and Washington.
"We agreed to launch the customs regulations for the [...] union on a bilateral basis," Putin told reporters at a briefing in Russia's second-largest city, St. Petersburg.
The absence of Belarus at the first stage of the customs union could also increase the likelihood of oil price disputes between Moscow and Minsk, which have previously led to the disruption of Russian oil flows across Belarus to Germany and Poland.
However, Putin said he hoped Belarus would join the union after the country had approved all of the required legal statutes.
"We will apply to the WTO in a trilateral format [in this case]. If it does not materialise we will apply together [with Kazakhstan]," Putin said.
He confirmed that there is a fundamental disagreement with Belarus over energy pricing as Russia has refused to abolish export duties on the oil it sells to Minsk, something analysts had seen as a the key reason for Belarus to join the pact.
Minsk has already offered to sell control of its major energy assets to Russian firms, but Russia does not believe this alone would solve existing problems in energy price talks.
Oil reserves in the Caspian basin are estimated to be worth several trillion dollars, and negotiations over the demarcation of the Caspian Sea have been ongoing for nearly a decade among the states bordering the Caspian - Azerbaijan, Russia, Kazakhstan, Turkmenistan and Iran.
(EurActiv with Reuters.)