Yushchenko said he hoped to smooth over longstanding differences with Moscow during a visit to Kyiv next month by President Vladimir Putin.
Putin, who has not visited Ukraine since early 2005, is expected in Kyiv in the second half of December.
"We do not want our moves toward the European Union to bring along two suitcases of problems in Ukrainian-Russian relations," Yushchenko said.
He also said that Ukraine -- a major transit country for Russian energy supplies to Europe -- would like an EU-Russia agreement on energy to include transit policy.
Poland this week blocked the start of talks on a EU-Russia partnership agreement, arguing that Russia should first lift a ban on Polish farm products and also give guarantees on energy supplies.