The EU said the meeting would ensure "a fully coordinated EU response to the situation," adding "we look to both parties to ensure that gas supplies to the EU remain unaffected".
The chief executives of the two companies held talks on Wednesday to hammer out a deal.
The news of the second cut was made after a 1700GMT deadline on Tuesday.
"Today Gazprom CEO Aleksey Miller and Naftogaz Ukrayiny CEO Oleh Dubyna held talks by telephone, in the course of which agreements have been reached to resolve the crisis with the supply of gas to Ukraine," Gazprom spokesman, Sergey Kupriyanov, said on Russian television.
"If the Ukrainian side does not return to the negotiating table, I do not exclude a further reduction in supplies," Sergei Kupriyanov, a Gazprom spokesman, said on state television.
Ukraine has agreed to pay for gas supplies for January and February of this year.
The dispute started after Russia said Ukraine had not paid its debts for previous deliveries, which Gazprom says totals $1.5bn (£770m).
But Gazprom said talks continued on other issues.
But Ukraine maintains the payments have already been made.
Gazprom cut supply twice this week, first on Monday by 25% then again by 25% on Tuesday.
Escalating crisis
Gazprom said it reduced supplies to Ukraine by 25% on Monday after talks broke down last week.
Monday's cut effectively ended supplies of gas directly from Russia, which make up a quarter of Ukraine's imports. The rest of Ukraine's imports comes from other states but travels through Russian pipelines.
[We look] to the parties to make every effort to find a rapid and durable solution to their disagreement ...and to ensure that gas supplies to the EU remain unaffected European Commission
Naftogaz, Ukraine's state gas company, earlier said it reserved the right to take "appropriate" action - and disrupt supplies to Europe that transit Ukraine - if Gazprom carried out the threatened additional cut.
But after the announcement, a spokesman said the firm had no plans for such a move at present thanks to warm weather and sufficient reserves.
European fears
Gazprom spokesman Sergei Kupriyanov reassured European gas users on Tuesday that shipments of Russian gas would continue.
Kiev's energy relationship with Russia is the one that matters, and that just seems to be getting worse Dominic Laurie, Europe business correspondent
"Export deliveries via Ukrainian territory are carried out in full volume," he said.
European Commission spokesman Michele Cercone said: "They [Gazprom] reassured us that gas supplies to the European Union will not be affected.
A National Grid spokesperson said the UK did not rely on pipelines crossing Ukraine for its gas. "The UK doesn't get any of its gas direct from Russia," he said.
Kiev tension
A previous row between the two sides saw Russia cut gas to Ukraine in 2006. It also hit exports to Western Europe and affected diplomatic relations between Brussels and Moscow.
A previous row between the two sides saw Russia cut gas to Ukraine in 2006. It also hit exports to Western Europe and affected diplomatic relations between Brussels and Moscow.
The BBC's Europe business correspondent Dominic Laurie says since that last crisis, a lot of work has been done to improve the relationship.
"Top officials meet often, and there's now an early warning system with Gazprom that alerts Brussels about dips in supplies at the Russian end," he said.
"The trouble is, the problems aren't there - but further west - in Ukraine. Kiev's energy relationship with Russia is the one that matters, and that just seems to be getting worse."
