"The merger proposal is in no way linked to the idea of the creation of a gas transportation consortium on a three-party basis and involving Russia, Ukraine and European firms. It is a separate proposal - more global, more large-scale," Gazprom's chief Alexei Miller said in a statement.
Russia's Prime Minister Vladimir Putin stunned Ukraine last month by proposing to merge Gazprom and Ukraine's Naftogaz to the surprise of industry experts and outcry of the Ukrainian opposition.
The move could give Moscow control over Kiev's gas transit network, which ships a fifth of Europe's gas consumption from Siberian fields and has been a headache for the Kremlin in past years when Kiev suspended supplies during pricing disputes.
But Ukraine's President Viktor Yanukovich said the European Union should be part of any talks between Kiev and Moscow to merge their gas groups
Relations between Moscow and Kiev have rapidly improved after February's presidential election in Ukraine, in which the pro-Western Ukrainian leadership lost out to Yanukovich, who is seen as more friendly towards Moscow.
Last month, the two countries reached accords on gas pricing and a lease extension for a key Russian naval base in Ukraine.
But Yanukovich has nevertheless insisted on involving both Russia and the EU in upgrades of Ukraine's ageing pipeline system as he called Brussels a partner of an equal if not bigger importance than Russia.
The European Union has responded by saying it would play no part in the Russian merger proposal.
Miller also said the merger would increase security of supplies to Europe but added that Gazprom would continue pressing ahead with South Stream, a pipeline designed to supply Europe's south, bypassing Ukraine.
On Thursday, Yanukovich shrugged off the threat from South Stream and said he was confident plans for modernising Ukraine's gas pipeline system were economically competitive.
Yanukovich met journalists ahead of a visit to Ukraine next week by Russian President Dmitry Medvedev.
(EurActiv with Reuters.)
"On the issue of a merger deal with Gazprom, 50-50 would be interesting for us, but it's clear that won't happen because Gazprom would never agree," Yanukovich said in an exclusive interview.
"Russia would not want to do that [...] But for us, a merger under any other conditions is impossible."
"Control can only be given in return for investment by Russia and Europe in the reconstruction of the existing gas transport system. Such investors would get a share of the property. But full Russian control, no, that's empty words," Yanukovich stated.