By Damian Grammaticas
BBC News, Moscow
Russian authorities say they intend to pursue a criminal case for bribery against Yulia Tymoshenko, the Ukrainian MP nominated as prime minister.
Yulia Tymoshenko backed Yushchenko throughout the protests
Ms Tymoshenko was one of the leaders of the street protests that forced a re-run of the presidential election.
The announcement comes two days after the presidents of Ukraine and Russia staged a public show of reconciliation.
But it appears there will be serious difficulties in their relations after Ukraine's "Orange Revolution".
Russia's prosecutor-general says his office will continue to pursue a criminal case against Ms Tymoshenko, even though she is now Ukraine's prime minister-designate.
A court has already issued an order for her arrest if she visits Russia.
Ms Tymoshenko has dismissed as politically-motivated accusations that she attempted to bribe officials in Russia's defence ministry when she ran a Ukrainian gas trading company back in 1996.
It is alleged she wanted the officials to inflate the price of supply contracts with the Russian military by $80m (£42.5m).
At the start of this week, Ukraine's new President, Viktor Yushchenko, visited Moscow in an attempt to smooth over differences with President Vladimir Putin, who had openly backed his rival in the disputed election.
It surprised many that on the same day, Mr Yushchenko announced he had chosen Ms Tymoshenko to head his government. The choice is controversial and was bound to irritate Russia.
Ms Tymoshenko was one of the most radical and most prominent leaders of the month-long street protests in Ukraine's capital Kiev during the dispute over the presidential elections.
It is thought Mr Yushchenko has picked her to be prime minister to reward her for her role, and in the belief she can force through radical reforms.
But she is seen as an Ukrainian nationalist, and so is likely to alienate people in the Russian-speaking east and south of the country who backed Mr Yushchenko's rival in the election and who have close ties to Russia.