NEW YORK — Mikhail Khodorkovsky, the jailed oil tycoon turned liberal martyr, was found guilty today of a second set of charges in a trial held up as a symbol of Russia’s compromised justice system.

The guilty verdict was widely expected but nonetheless provoked harsh condemnation from Russia’s marginalized opposition, international observers and Khodorkovsky’s family.

“We were expecting and preparing for a guilty verdict, but it still came as a shock,” said Pavel Khodorkovsky, the tycoon’s 25-year-old New York-based son. “Up until last night, I was hoping the judge would take a stand, I was hoping he would make a brave decision.”

Reading the verdict to a packed Moscow courtroom, Judge Viktor Danilkin said Khodorkovsky and his business partner, Platon Lebedev, had engaged in embezzlement and money laundering.

U.S. Secretary of State Hillary Clinton said the conviction “raises serious questions about selective prosecution.”

“This and similar cases have a negative impact on Russia’s reputation for fulfilling its international human rights obligations and improving its investment climate,” Clinton said in a statement.

The nearly two year-long trial has been marked by delays and procedural absurdities. The verdict was initially set to be read on Dec. 15 and then postponed without explanation until today, when most of Russia’s foreign press corps had quit the country for the holidays.

“By all accounts, the rule of law in the conduct of this trial has been abandoned,” Richard Ottaway, a Conservative British MP, said in a statement. “This has serious implications for the confidence of overseas investors.”

Khodorkovsky was one of a dozen men who grew unfathomably wealthy by capitalizing on the chaotic aftermath of the Soviet Union’s collapse. His dramatic arrest in 2003 sent a signal to Russia’s oligarchs that the Kremlin was re-asserting control over the country’s economy. Found guilty of fraud and tax evasion, Khodorkovsky saw his Yukos oil company dismantled and sold off at fire-sale prices, landing mainly in the lap of state-run oil firm Rosneft.

A U.S. diplomatic cable released by Wikileaks today showed the U.S. government views the case as one of selective justice. “It is not lost on either elite or mainstream Russians that the GOR [government of Russia] has applied a double standard to the illegal activities of 1990s oligarchs; if it were otherwise, virtually every other oligarch would be on trial alongside Khodorkovsky and Lebedev.”

Vladimir Putin, who was president when Khodorkovsky was arrested, is said to harbor a personal hatred for the jailed tycoon. Mikhail Kasyanov, who served as prime minister under Putin, said Khodorkovsky’s funding of mainstream opposition parties without Kremlin approval sealed his persecution.

Khodorkovsky’s current sentence runs out in October 2011, on the eve of parliamentary elections and half a year ahead of the country’s next presidential vote. The current charges could keep Khodorkovsky and Lebedev in jail through 2017. The reading of the 250-page verdict is expected to last several days, ending with sentencing. Khodorkovsky’s lawyers have mused that the sentence could be handed down on New Year’s Eve, when public attention will be lowest.

“The trial was a charade of justice, the charges were absolutely false, but I fear the sentencing will be very real,” Vadim Klyuvgant, Khodorkovsky’s lead lawyer, said in a statement.

If Khodorkovsky’s arrest signaled the Kremlin’s new rules for business, his trial became a potent symbol of the murky workings of Russia’s justice system. It’s a dim view that has been reinforced by several high-profile cases, including the arrest and subsequent death in prison of lawyer Sergei Magnitsky in 2009.

“My dad is a bellweather and his case is a test for Russia,” said the younger Khodorkovsky, who has not seen his father since September 2003, one month before the tycoon’s arrest.

Buoyed by a sizeable team of Western public relations agents and hampered by lack of access to state-run television in Russia, Khodorkovsky’s cause has always garnered more attention abroad than at home. The collapse of the Soviet Union threw many Russians into poverty, leaving no love lost for the men who grew wealthy from it.

Yet after seven years in prison, some of it at a Siberian labor camp, Khodorkovsky’s image has changed and even Russians have begun to take notice.

Research released by the Levada Center, a Russian pollster, earlier this month found that 7 percent of Russians followed the case “rather closely” — up from 4 percent in May. While in May 75 percent of those polled said they had never heard of the case, in November that number dropped to 65 percent.

At least 100 people gathered outside the courtroom on Monday, calling for Khodorkovsky’s release.

Khodorkovsky has aimed to hold himself up as the voice of Russia. In his final statement to the court in November, he issued an emotional appeal for justice, equating his fate with that of the nation. “Much more than two people’s fates lie in your hands,” he said. “Right here and right now, the fate of every citizen of our country is being decided.”

The leaked U.S. cable, written in December 2009, shows that the U.S. government viewed the case as politicized. “The fact that legal procedures are apparently being meticulously followed in a case whose motivation is clearly political may appear paradoxical,” the cable reads. “It shows the effort that the GOR is willing to expend in order to save face, in this case by applying a superficial rule-of-law gloss to a cynical system where political enemies are eliminated with impunity.”

President Dmitry Medvedev, a former lawyer, vowed to reform Russia’s justice system upon coming to power. Yet he continues to play second fiddle to Putin, who many believe will return to the presidency in 2012.

During a televised question-and-answer session with the Russian people earlier this month, Putin commented on the Khodorkovsky trial, saying he believed that “a thief should sit in jail.” Medvedev appeared to criticize the move one week later, saying in a traditional end-of-the-year interview with state-run television that “neither the president nor any other state official has the right to comment on this particular case before the verdict is passed.”

The case only points to Medvedev’s impotence, Khodorkovsky’s lawyers said in a statement. “The trial and its verdict are an open challenge — indeed an affront — to President Dmitry Medvedev's highly-publicized efforts to ensure the rule of law and to reform Russia's criminal justice system and to fight government corruption.”

Khodorkovsky’s son agreed: “What happened today shows that figuratively Putin won and Medvedev lost.” He said he doubted his father would be released while Putin remained Russia’s foremost authority.

“He definitely wants to stay in Russia, however I don’t know what he would do if a deal would be on the table,” the younger Khodorkovsky said of his father. “Seven years in prison is no joke. I would want my father to leave because I think he has suffered well beyond any reason. He shouldn’t continue to pay with his life for his political support for democracy.”

Protesters outside the court where Khodorkovsky's verdict was read:

Editor's note: This story was updated to add comments from U.S. Secretary of State Hillary Clinton and Pavel Khodorkovsky.