Platon Lebedev, a key shareholder with Yukos, has been in jail since 2 July on charges of embezzlement from a controversial 1994 privatisation deal.
The move threatens to reignite an old conflict between the company and the Kremlin.
Before the new charge was added though, there were suggestions last week that Lebedev could be released as early as Tuesday.
Russia’s Prosecutor General Office said on Monday it was adding tax evasion – the fourth charge against Lebedev. He is also accused of stealing state property.
The high-profile investigation rattled the Russian market. Russia's central bank has reported a $900 million decline in its reserves, which economists attribute to the flight of capital following the Yukos affair.
But the attack on Yukos has been interpreted as a Kremlin warning to CEO Mikhail Khodorkovsky, and Russia's wealthiest oligarch, to stay out of politics and prevent him from wielding influence in the Duma, the lower house of parliament.
The pursuit of Yukos has left foreign investors nervous about the stability of companies formed on the basis of the controversial and non-transparent privatisation deals of the 1990s.
Arkady Volsky, the head of the Russian Union of Industrialists and Entrepreneurs, said at a Kremlin meeting with Russian President Vladmir Putin, senior MPs and regional leaders that he feared such investigations could lead to instability.
“We had a normal, stable situation, but actions upsetting the situation have begun,” Volsky said.
“I ask the law enforcement agencies not to make the situation explosive,” he said. He added that he did not want to interfere in the work of prosecutors, but questioned “why they first put someone in jail and then figure out what’s going on, and not vice versa.”
Prosecutors are also investigating five cases of murder and assassination attempts related to Yukos.