BRUSSELS—Russian gas monopoly OAO Gazprom still aims for an amicable settlement of the European Union's antitrust case against the company, Deputy Chairman Alexander Medvedev said Thursday following a meeting with the EU's competition commissioner.

Mr. Medvedev said the company disagrees "in particular" with one point of the commission's charges, which accuses the company of charging customers in some Eastern European countries excessive prices for natural-gas shipments.

"Our prices are nearing a record low for our customers across Europe," Mr. Medvedev said in a statement.

Mr. Medvedev said his meeting Thursday with the EU's Competition Commissioner Margrethe Vestager, the first since charges were filed against Gazprom in April, was "productive."

"As I have stated in the past, we prefer to settle this case amicably and will continue to engage with DG Competition [the EU's antitrust body]," Mr. Medvedev said.

"Today's meeting provided a good framework for future discussions and we hope to make swift progress toward a mutually acceptable solution."

A commission spokesman confirmed the meeting between Ms. Vestager and Mr. Medvedev, saying the two had an "informal exchange on Gazprom's preliminary views" on the charges that have been filed against the company. He declined to comment further.

Settlement talks between the commission, the EU's antitrust watchdog, and Gazprom broke down early last year, when the conflict in eastern Ukraine hurt relations between Brussels and Moscow.

The commission usually gives companies that have been hit with antitrust charges a chance to meet with the commissioner and other officials to find out more about the cases against them. Gazprom has until mid-September to send a formal response to the charges.

In late April, Ms. Vestager announced antitrust charges against Gazprom, claiming its often-secretive contracts were hindering competition in the natural-gas markets in eight EU countries—Bulgaria, the Czech Republic, Estonia, Hungary, Latvia, Lithuania, Poland and Slovakia.

In five of those countries—Bulgaria, Estonia, Latvia, Lithuania and Poland—the EU also accused Gazprom of charging unfair prices by using complex formulas that link the price of gas to that of oil. In certain periods, Ms. Vestager said at the time, these methods led to prices that were 40% higher than the charges of competitive gas hubs.

The sharp drop in oil prices over the past year has pushed down the cost of gas in countries where contracts with Gazprom are still governed by the pricing formulas.

The commission also alleged that in Bulgaria and Poland Gazprom has sought to link the supply of gas to controlling key infrastructure projects, including the now-abandoned South Stream pipeline and the Yamal-Europe pipeline.

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

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