The warning came less than 24 hours after a meeting between Russian President Vladimir Putin and his Ukrainian counterpart Petro Poroshenko as well as Europe's main energy diplomat Guenther Oettinger, which included talks to secure Russian gas flows during the peak demand winter.
Read MoreUkraine's Poroshenko talks tough ahead of meetings with Merkel, Putin
Although Russian officials and state-controlled gas company Gazprom were not immediately available for comment, a Russian source said it would be more likely that Ukraine would start taking gas intended for the EU to meet its own demand than for Russia to cut off supplies to Europe.
"It's unlikely that Russia would cut gas supplies. Ukraine will start siphon off it itself, as it has been the case in the past," a senior source at the Russian Energy Ministry said.
"We have a Plan B for the worst-case scenario. But we don't expect to need it," European Energy Commissioner Guenther Oettinger said in Ungheni, Moldova on Wednesday.
Third cut in a decade
Russia halted gas supplies intended for Ukraine in June over a pricing dispute, but has continued supplies via the country that are contracted to customers in the EU, which make up around 80 percent Gazprom's gas sales.
Russian gas flows to Ukraine have now been halted three times in the past decade, in 2006, 2009 and 2014, due to price disputes between Moscow and Kiev, and flows to the EU were disrupted in 2006 and 2009 after Ukraine took some of the gas intended for the EU to meet its own winter demand.
European and Ukrainian power and gas providers have been preparing for a potential Russian supply cut by injecting as much gas as possible into storage over the low demand spring and summer seasons, and there have also been improvements to infrastructure that would allow Ukraine to receive some gas from within the EU.
"The government has amassed 15 billion cubic metres (bcm) of gas in storage," Yatseniuk said, and the government has plans to boost storage to 25 bcm.
"Europe now has 16.52 bcm (31.2 percent) more gas in storage compared to the same time last year," research firm Energy Aspects said, but added that "based on recent average rates of injection, Ukraine will only fill its storage to around 52 percent of capacity come the start of withdrawal season."
Due to a lack of alternative supplies, analysts say Ukraine and central and southeastern European countries with no alternative to Russian gas supplies via Ukraine would not be able to cope with a winter gas cut without large-scale energy supply disruptions.
Russian gas is key
Russia is Europe's biggest supplier of oil, coal and natural gas, meeting around a third of demand for all those fuels, according to Eurostat data, and receives in return some $250 billion a year, making up around two-thirds of government revenue.
Last year, half of Russian gas exports to the EU were shipped via Ukraine.
Gazprom declined immediate comment and the Energy Ministry was not immediately available to comment.
Read MoreUkraine may have an energy problem besides nat gas
While buyers can switch oil and coal suppliers relatively quickly and easily, Europe receives most of its gas through pipelines that are fed by only one supplier, Gazprom, in annual exports worth $80 billion.
"Our main concern, no doubt, is gas. We have ongoing ... negotiations between the Russian Federation and Gazprom on one hand and Ukraine and (Ukraine's gas company) Naftogaz and our European Commission," Oettinger said after meetings with Ukrainian and Russian officials during the night of Tuesday and Wednesday.
"On Friday we will be in Moscow for the next trilateral consultation between the Russian Federation/Gazprom and Ukraine/Naftogaz with the EU as a moderator of important process," he added.
The latest gas pricing dispute is closely intertwined with a bigger standoff between Moscow and Kiev.
Ukraine's Moscow-leaning president Viktor Yanukovich fled his country following weeks of street clashes by people angry that he had rejected an association agreement with the EU.
Moscow subsequently annexed Ukraine's Crimea peninsula in March, while pro-Moscow separatists have staged an insurgency in the east of the country.
Read MoreRussian defense ministry denies any incursion into Ukraine
The area where the fighting is concentrated, known as the Donbass, is a major source of coal for Ukraine.
Yatseniuk said the government has been trying to diversify coal supplies as "Russia and their mercenaries are bombing and destroying mines". Russia has denied any involvement in the conflict.