Russia's national independent media is closing down
The highest court of arbitration in Moscow upheld an earlier ruling that the station should close because it was losing money - the request of a minority shareholder.
The main shareholder in TV-6 is a well-known critic of the president - former Kremlin insider Boris Berezovsky.
A TV-6 spokesman said the day would be remembered as "black Friday".
TV-6 was a relatively unknown station until last year, when it was revamped by journalists arriving from the popular NTV channel after a battle with the government.
In a tense confrontation with journalists last year, NTV was sold to government-owned giant Gazprom and its board of directors dismissed.
NTV had been carrying critical comments about Moscow's handling of the war in Chechnya.
Debts
The case against TV-6 was brought by a subsidiary of another oil company - LUKoil - a minor shareholder also closely linked to the government.
It demanded that the station be liquidated because its debts outweighed its assets.
The judges have given no details on how they reached their ruling.
The majority shareholder, Boris Berezovsky, described the decision as "unlawful and unconstitutional," but said he was not surprised.
"This is not a dispute between businesses but pure politics. The authorities will use any means to win the fight for the channel," he said.
In a similar vein, TV-6 Deputy director-general Pavel Korchagin told the BBC that the Russian government considered all independent media outlets "a potential threat".
Stations spokeswoman Tatyana Blinova said the liquidation process could begin as early as Monday.
However she said the station could appeal to the constitutional court under new legislation that came into effect on 1 January barring a minority shareholder from calling for a company's liquidation.
The BBC's Russian affairs analyst, Stephen Dalziel says dismissive statements by the Kremlin that this was a matter of business, not politics, look increasingly implausible.
Some of TV-6 programmes were strongly critical of President Putin and other top government officials.
Media control
The case has renewed Russian and international concern about the freedom of media in Russia.
Russian opposition politicians and journalists have criticised the move, which they see as a further attempt by the government to smother Russia's independent media.
The government denies any interference, but the BBC's Nikolai Gorshkov in Moscow says the Russian public has developed a fairly cynical attitude to whatever comes out of the Kremlin.
Questions are being asked as to why Mr Putin does not move against other tycoons, our correspondent says.
On Wednesday, the United States expressed its concern over the court hearing into the TV-6 case.