The energy ministers of Russia and Ukraine agreed Monday that a dispute over natural-gas deliveries to some rebel-controlled territories in eastern Ukraine won't affect supplies to the rest of the country and the European Union.

The spat between Ukrainian state gas company OAO Naftogaz and its main supplier, Russia's OAO Gazprom, had endangered an EU-mediated deal that was meant to secure gas supplies during the cold winter months. It also raised questions on whether the two sides would be able to negotiate a follow-up arrangement to regulate deliveries over the summer months once the winter deal expires at the end of March.

The agreement, following talks between the two ministers in Brussels, doesn't resolve the question of who will ultimately pay for gas delivered by Gazprom to the Donetsk and Luhansk regions but not authorized by Naftogaz. Russian has been backing the rebels in those regions.

The pact obliges the two sides to sort out the issue without taking hostage far-greater supplies to the rest of Ukraine and the EU.

"I am reassured that the supply of gas to the EU markets remains secure, " said Maros Sefcovic, the European Commission's vice president for energy, who presided over Monday's negotiations. Russian Energy Minister Alexander Novak and his Ukrainian counterpart, Volodymyr Demchyshyn, also agreed that they would start talks on deliveries beyond March before the end of the month.

"We agreed to discuss questions of summer gas supplies and gas pumping into [Ukraine's gas storage] at the end of March," Mr. Novak said in a statement distributed through his ministry's Twitter account.

Naftogaz had complained in recent weeks that Gazprom had unilaterally cut deliveries and that damage to pipelines in territory controlled by pro-Russian rebels prevented it from verifying deliveries there. Gazprom, meanwhile, warned that a failure by Naftogaz to prepay for agreed volumes could leave Ukraine--and the EU--without fresh gas within days. It said that it had continued supplies to Donetsk and Luhansk for humanitarian reasons.

After the talks, the two sides agreed that Naftogaz would continue to pay in advance for deliveries for domestic consumption in Ukraine and guarantee uninterrupted transit to the EU. However, shipments to Donetsk and Luhansk that haven't been authorized by Naftogaz won't be subtracted from those advance payments and instead will be resolved separately.

"This will be the subject of special volume verification and negotiations," Mr. Novak said in his Twitter statement.

Monday's deal removes the threat of immediate supply shortages. But difficult negotiations are ahead on how much Ukraine should pay for gas from Russia after March and how its large storage facilities, which are key to ensuring supplies to Europe during the winter, will be replenished during the summer months.

Ukraine has in recent months reduced its dependence on direct deliveries from Moscow thanks to increased shipments from Slovakia and other EU countries.

Write to Gabriele Steinhauser at gabriele.steinhauser@wsj.com

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