Members of the government's Investigative Committee searched the homes of Khodorkovsky's spokeswoman Kulle Pispanen and employees of his opposition group Open Russia.
The group, citing the Investigative Committee, said the searches were connected to an old case over the allegedly fraudulent privatisation in 1994 of a mining and fertiliser company.
The 2003 case led to the criminal prosecution of one of Russia's most powerful oligarchs and the dismemberment of his Yukos oil company which have become defining events in the presidency of Vladimir Putin.
"This is rather funny, especially taking into consideration that none of Open Russia's current employees and activists worked at Yukos," he said on Echo of Moscow radio, noting that some of his staff were children in the 1990s.
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"Insanity is entering its final stages," Khodorkovsky, who spends much of his time in London, added, referring to the authorities.
Liberal lawyer Pavel Chikov said the apartments of at least seven people had been searched including those of several Saint Petersburg-based Open Russia coordinators.
The Investigative Committee, which reports to Putin, confirmed the early morning raids.
Mikhail Roskin, a 24-year-old Open Russia employee based in Saint Petersburg, said investigators searched the apartment of his relatives.
The link to the 2003 case was dubious at best, he added. "I was 12 then," he told AFP. "Back then I cared about everything except Khodorkovsky or politics."
Earlier this month Russian investigators charged the former oil tycoon in absentia with organising the 1998 murder of a mayor in Siberia, a move supporters say is aimed at silencing the self-exiled Kremlin critic.
Once Russia's richest man, Khodorkovsky, 52, spent a decade in prison on charges of tax evasion, fraud and embezzlement which he and his supporters say were trumped up in revenge for the business magnate's political ambitions.
Khodorkovsky was unexpectedly pardoned by Putin in 2013 and flown out of the country.