"Nabucco is not a direct competitor of South Stream," Oettinger told a conference in reference to a Russian-backed project that is also designed to transport natural gas to highly-dependent western European markets.
The path Nabucco is supposed to take, from the Caspian Sea via Turkey and eastern Europe, bypasses Russia and Ukraine, which have argued over transit rights in the past, cutting supplies to Europe in the middle of winter.
South Stream is backed by Russian gas behemoth Gazprom.
"I appreciate Russia as a partner for Russian gas, but for gas from third countries I prefer the shortest route and not a path that makes a detour via Russia," as is the case with South Stream, Oettinger said.
The Nabucco project has been approved by European Union officials but has not yet signed the contracts with producer countries it needs to ensure it is economically viable.