The gesture is largely symbolic because Russia has dismissed similar Ukrainian claims.
But it underscores the severe tensions between the two neighbours and potentially complicates the solution of a litany of existing trade disputes.
The westward-leaning former Soviet country's Anti-Monopoly Committee said Gazprom had two months to pay USD 3.5 billion for abusing the "monopoly status" it enjoys on gas transits through Ukraine.
The committee's deputy chief Mariya Nyzhnyk said the sum represented 30 per cent of the price for natural gas that passed through the country over the past five years.
"Gazprom intends to defends its rights and legitimate interests by all legal means at its disposal," it said in a statement.
Ukraine's decades-old pipelines account for about 15 per cent of all gas imported by the European Union -- its members rely on Russia for about a third if their outside supplies.
Some of Gazprom's EU clients saw their deliveries limited in 2006 and 2010 when the state-run behemoth - long accused of raising the rates of neighbours who want to ease their dependence on Moscow - halted supplies to Ukraine over price disputes.
Ukraine has been weening itself off Russian energy imports and purchased almost no gas from its eastern neighbour in the period mentioned by Gazprom.
But the Russian firm said the amount it was after fell under the take-or-pay scheme that requires clients to reimburse Gazprom for any contracted gas they failed to purchase in a specific timeframe.
Russia's latest charge brings to nearly USD 32 billion the bill it claims is due by Kiev.
Kiev authorities have vowed repeatedly not to halt shipments to Europe despite its multiplying disputes with Gazprom.