Yanukovych also said Ukraine will not join a customs union with Russia, something the EU has said would scupper the plans for an EU-Ukraine free-trade zone.
He reiterated Ukraine's determination to join the World Trade Organization.
The Ukrainian prime minister also defended his decision to put ties with NATO on ice, saying it has the support of the governing coalition in the Rada.
Yanukovych's position on NATO has, however, been attacked by President Viktor Yushchenko and Defense Minister Anatoliy Hrytsenko.
Yanukovych said Ukraine's domestic priorities will be to fight against corruption and to pursue economic reforms.
Yanukovych was in Brussels last week, but returned to meet European Commission President Jose Manuel Barroso who was out of town on the Ukrainian Prime Minister's first visit.
Barroso today reiterated the EU's current offer to Ukraine: closer ties with no mention of membership.
"Our objective is to bring Ukraine closer to the European Union," Barroso said. "Our objective is also to support political, institutional and economic reforms in a way [that would] contribute to economic growth and the improvement of the living standards of Ukrainian citizens."