Prime Minister Arseniy Yatsenyuk said the investigation was opened after the government went to court over the alleged embezzlement.
The government wants to find out what happened to USD 256 million worth of public funds that it says went missing in a deal between Naftogaz and the Ostchem chemical firm, owned by Dmytro Firtash.
Firtach is currently under house arrest in Vienna where a court is due to rule on Thursday on a demand to extradite him. The United States issued a warrant for him last year on charges of corruption linked to titanium mining in India.
The interior ministry said a court upheld its demand to impound 500 million cubic metres of gas belonging to companies owned by Firtash and his associate Sergei Levochkin.
Levochkin was a senior adviser to Ukraine's pro-Russian former president Viktor Yanukovych, who was ousted last year after an uprising by pro-European protesters.
Under pressure from its Western allies, the government elected after Yanukovych's departure is cracking down on corruption and oligarchs as it tries to reform Ukraine's economy.
A close ally of Yanukovych, Firtash made a fortune importing gas to Ukraine from Russia and Central Asia via his group Rosukrenergo in collaboration with Russian gas giant Gazprom.
Rosukrenergo was liquidated last year after widespread allegations of corruption.
One of Firtash's surviving businesses, DF, in a statement on Wednesday rejected the government's lawsuit as part of "a long-planned campaign of political persecution" against him.
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