Authorities said Ulyukayev was detained on Tuesday during an operation by the FSB security service and that President Vladimir Putin was informed of the investigation.
The detention came a day after the minister allowed state oil giant Rosneft to acquire a majority stake in another Russian oil company and allegedly received money for the endorsement.
"This is about extortion of a bribe from Rosneft representatives accompanied by threats," Investigative Committee spokeswoman Svetlana Petrenko said.
Ulyukayev, she said, was caught red-handed as he received the bribe and that he would be charged shortly.
"This is a very serious accusation that requires very serious proof. In any case only a court can decide," Kremlin spokesman Dmitry Peskov told Interfax news agency.
Russian news agencies said Prime Minister Dmitry Medvedev has called for painstaking investigation into the case and and discussed the investigation with President Putin.
They said Ulyukayev was detained as part of "sting operation" after investigators received "serious evidence" from "tapping his conversations and the conversations of his associates."
The controversy revolves around Rosneft's acquisition of a 50.07 percent stake from the state in Bashneft in a $5.2 billion deal last month.
The sale came after months of wrangling that saw Rosneft face opposition from many in the government, who have demanded the country's economy be liberalized.
The Bashneft sale "confirms that Russia is knowingly building state capitalism and monopolizing the economy," leading business daily Vedomosti said at the time when the deal was signed.
"It's impossible to call the sale of one state company to another state company privatization," it added.
It was said at the time that the government had received only two bids and the other one had been less than Bashneft's independently assessed value.
In September, President Putin voiced his concern over the potential seizure of one state-controlled company by another.
“Probably it’s not the best option when one company under state control acquires another purely state company,” the Russian leader said.
Bashneft, an oil producer based in the central city of Ufa in the Russia’s southwestern Republic of Bashkortostan, was originally privatized in the early 2000s.
In late 2014, however, a Moscow court ordered the nationalization of a Bashneft’s stake of some 72 percent held by billionaire Vladimir Yevtushenkov after he was jailed on money laundering charges.
Bashneft operates 140 oil and natural gas fields in the country and has an oil production of 16 million tonnes annually.
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