Barroso's "threats" came a day after Russian gas exports to Europe came to a halt again in view of a fresh dispute between Russia and Ukraine.
Moscow is accusing Kiev of not abiding by a deal signed only a day earlier to facilitate gas transit through Ukraine.
A senior official of Gazprom - the Russian state energy provider - claimed on Wednesday that Ukrainians were refusing to allow gas transit under conditions laid down by the deal.
Despite the recent transit deal, gas flow to Europe has not yet been normalised.
Russia resumed gas supplies on Tuesday after agreeing to a deal with Ukraine and the EU, only to shut them off again hours later.
Gazprom said in a statement that Naftogaz - the Ukrainian state energy firm - "refused to accept Russian gas" at one of the main entry points to the Ukrainian transit system.
The head of Naftogaz said they would not resume the deliveries of gas in view of conditions set by Gazprom.
The route, the official said, would force Naftogaz to halt supplies to Ukrainian consumers.