Khodorkovsky, who heads the Russian oil giant YUKOS and is Russia's richest man, was seized by police on Saturday morning at a Siberian airport as his plane briefly halted to refuel.
The tycoon was then flown to Moscow for questioning by prosecutors.
He was then charged with seven counts of tax evasion and fraud. A Russian court later ordered Khodorkovsky's detention.
A spokeswoman for the Russian Prosecutor General's Office said Khodorkovsky was detained after he failed to respond to summons to appear on Friday.
Conflict with Putin
The spokeswoman made no mention of the bitter political conflict the oil magnate has been embroiled in with Russian President Vladimir Putin in asdance of parliamentary elections in December.
The Kremlin suspects Khodorkovsky of funding political opponents of Putin.
"Khodorkovsky was summoned for questioning on Friday but deliberately and without explanation ignored the summons. Consequently, it was decided to oblige him to appear"
Khodorkovsky, for his part, has acknowledged funding two liberal parties competing with Putin's allies for seats in parliament.
Shortly after the YUKOS chief's arrest, company spokesman Alexander Shadrin said investigators were trying to question the tycoon without his lawyers being present.
Shadrin said Khodorkovsky's aircraft was approached by armed special police officers. He was ordered out of the plane and taken away.
YUKOS has been in the Kremlin's sights for some time.
Two of its major shareholders currently face charges in connection with prosecutors' investigations.
One is charged with theft of state property and the other with tax evasion.