MOSCOW — Russia’s most eminent scientists delivered a rare rebuff against Vladimir Putin yesterday when they voted to keep one of the prime minister’s most influential allies out of their academy.

The decision by the Russian Academy of Sciences to reject Mikhail Kovalchuk’s application for full membership as an academic represented an unusual act of rebellion in the face of intense Kremlin pressure.

Critics say it could undermine Mr. Putin’s alleged ambitions to exert total control over Rosnanotech, a multibillion-dollar state enterprise dedicated to nanotechnology, that Mr. Putin created last year.

Last June, Mr. Kovalchuk was appointed head of Rosnanotech, which received about $5.2 billion in government funding in its first year alone. But without full membership of the academy, he cannot be confirmed as official head of Rosnanotech, and will therefore have to remain its acting chairman — making him more vulnerable should Mr. Putin’s grip on power weaken.

Critics claim that Rosnanotech is an opaque organization whose purpose is to channel funds into private offshore bank accounts. Mr. Kovalchuk’s brother Yuri has been a close friend of Mr. Putin since the early 1990s. Along with several other associates, they built country houses next to each other on a lake near the city as part of a project known as the “Ozero dacha collective.” They have been accused of transforming themselves into a new generation of “state oligarchs” and include Gennady Timchenko, a co-founder of the Gunvor group, the world’s third-largest oil trader with an annual revenue of $72 billion.