Ulyukayev, 61, was arrested in November 2016 while still a minister, the first time in decades an acting cabinet member had been detained and criminally charged.
He denies having taken a $2 million kickback (1.7 million euros) to clear state oil giant Rosneft to acquire a stake in oil firm Bashneft.
On Tuesday, a federal prison service car took Ulyukayev from his home, where he is under house arrest, to Moscow's Zamoskvoretsky district court. Tuesday's hearing was a preliminary closed session to determine how the trial would proceed.
Asked by journalists outside the courthouse if he acknowledged his guilt, Ulyukayev said: "What do you think? Of course not."
Looking visibly thinner, the ex-minister said he had lost 14 kilogrammes in the course of the case. "Thanks to our justice system.
"I did not take bribes," he insisted as he got into the car that would take him back to his home. "It's all a provocation."
Investigators say Ulyukayev demanded a bribe from Rosneft and was caught red-handed accepting the cash. The identity of the person who allegedly paid the bribe however has not been revealed.
Sources say Ulyukayev was under surveillance by the security service, who had also tapped his phone.
If convicted, he faces up to 15 years in prison.
Tuesday's hearing set the next court date for August 16, when Ulyukayev will be expected to make a formal plea.
The court also ruled to extend Ulyukayev's house arrest by another six months, until late January of next year.
Ulyukayev's arrest was greeted with shock and bewilderment in Russia, unleashing speculation that it could be part of a power struggle inside the government ahead of next year's presidential elections.
Prime Minister Dmitry Medvedev at the time called the arrest "a grave event... beyond my comprehension" which proves that no official is immune to prosecution if he engages in corruption.
An uncharismatic official, Ulyukayev had been charged with the daunting task of pulling Russia out of economic crisis, and was considered part of the liberal wing of the government.
He had initially opposed the sale of the 50.07-percent stake in Bashneft to Rosneft, which is headed by Igor Sechin, a powerful ally of President Vladimir Putin.
He later endorsed it however after Putin said it could help fill state coffers.
Following his arrest he was quickly dismissed from his ministerial post in a decree issued by Putin. He was replaced by a 35-year-old economist Maxim Oreshkin, who had been working at the finance ministry.
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