In 2012, Putin fired the then defence minister, Anatoly Serdyukov, the highest-ranking official ever to be removed over corruption allegations.
According to the Investigative Committee, the minister's department had been given the responsibility of overseeing a sell-off of state assets - including the government's 50 per cent stake in oil producers Bashneft.
Mikhail Zygar, a prominent journalist and author of a best-selling book on Putin's inner circle, says Ulyukayev's fall from grace could be Putin's tactic to balance a perceived growing influence of liberals in the government with the more conservative group of intelligence and security officers.
The minister also predicted last week that fourth-quarter figures for the Russian economy would be "visibly" more positive after more than two years of contraction.
Russian state-owned television early Tuesday ran Ulyukayev's detention as the top story headlined "Fight on corruption", featuring comment from lawmakers who lauded the investigation as a major breakthrough in the long-anticipated clampdown on official graft.
The Minister was caught red-handed at the moment, when he was receiving a bribe, amid an investigative experiment.
There had been a widespread consensus that the Bashneft stake had been sold to Rosneft for a market price, so it was odd that a bribe would be given for a valuation that everyone agreed on anyway, he said.
Russian Minister of Economic Development Alexei Ulyukayev, who was detained over night, was formally charged with bribery by investigators, Russia's Investigative Committee spokeswoman Svetlana Petrenko said. "Nevertheless, if investigators and the court prove him guilty, this would be inexcusable", Titov was quoted as saying by RIA Novosti. "The overnight arrest of a minister lets everyone know that anything can happen at any time", Grigory Yavlinsky, leader of liberal opposition party Yabloko, told Russian radio station Ekho Moskvy.
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Putin's critics insist he has turned a blind eye to widespread corruption as his close allies have amassed vast fortunes during his time in power.
The oil deal that led to Ulyukaev's arrest has been at the center of a struggle at high levels of the government for months. The officials said Mr. Ulyukaev had been under investigation for more than a year.
Russian anti-corruption body revealed that the economy minister is corrupted.
Bashneft, an oil producer based in the central city of Ufa, was originally privatised in the early 2000s.
Two months after Bashneft's nationalisation, Yevtushenkov was released.
He allegedly took money for allowing oil giant Rosneft to buy a stake in another oil company, Bashneft.
Leading business daily Vedomosti said ahead of the confirmation of the Bashneft sale that it "confirms that Russian Federation is knowingly building state capitalism and monopolising the economy".
Mr. Ulyukaev spoke out against the deal in August, saying privatization of one state company by another was inappropriate.