"Despite pressure from the president, I will not allow any conflict over the Black Sea Fleet," Tymoshenko told reporters.
Yushchenko announced earlier this year that Ukraine would not extend the lease of the Russian naval base in Sevastopol beyond 2017.
After several ships from the fleet left the base in August to support Russia's operation to "force Georgia to peace," following an attack by Georgian forces on breakaway South Ossetia, Ukrainian President Viktor Yushchenko took an "aggressive stand" and signed a decree requiring prior notification from Russia of all movements by naval vessels and aircraft from Sevastopol.
Russia immediately responded to this move by saying Yushchenko's decree violated prior bilateral agreements on the deployment of the fleet in the Black Sea and Ukrainian territory.
Tymoshenko said that by opposing Russia, Yushchenko was trying to win over Ukrainian voters in the run up to presidential elections slated for the end of 2009.
According to Ukrainian popularity polls, Tymoshenko currently enjoys at least 25% of voter support. Leader of the oppositional Party of Regions Viktor Yanukovych is trailing with 20%, while President Viktor Yushchenko's popularity rating has plummeted to a mere 5%.
Relations between President Viktor Yushchenko and Tymoshenko have become strained recently after the prime minister failed to condemn Russia's actions in the conflict in South Ossetia, and back the president in his support for Georgia.
The premier, who was accused by the president of "treason and political corruption," was widely expected to run against Yushchenko at the next presidential election, but last week she said in a televised address to the nation that she was prepared to back out of the presidential elections "to support a single [democratic] candidate" in order to save Ukraine from further political turmoil.