Svetova, 57, who writes hard-hitting articles for opposition media including New Times magazine, has focused on writing about prisoner abuse in high-profile cases.
Svetova, 57, who writes hard-hitting articles for opposition media including New Times magazine, has focused on writing about prisoner abuse in high-profile cases and has interviewed many of them in jail.
Until last year, she was a long-time member of a public commission that monitors jail conditions in Moscow.
Russia's Investigative Committee in a statement said its officers had information that Svetova had documents about the "transfer to Russia and subsequent spending of money previously stolen by Khodorkovsky and his accomplices."
It stressed the search was "not linked to Svetova's professional activities or rights activism."
A source familiar with the situation told Interfax news agency that the search was "ordinary routine work that will not lead to any procedural status for the rights activist (Svetova)."
Khodorkovsky was arrested in 2003 after openly opposing Vladimir Putin during his first term as president, and went on to spend a decade in jail on tax evasion charges. He now lives in London.
The Yukos case under investigation on Tuesday concerns embezzlement from the state and dates back to 2003, said rights lawyer Anna Stavitskaya, who went to Svetova's flat to support her.
The Investigative Committee said the search was part of a continuing investigation into alleged "stealing of the assets" of Yukos and the Russian state "and their subsequent legalisation" by the oil company's former leadership and owners.
The search appeared to be linked to "the main Yukos case," Khodorkovsky's Open Russia foundation said on its website.
Svetova has published articles on Open Russia's website.
Khodorkovsky wrote on Twitter: "They've come to search Zoya Svetova's flat over the Yukos case... They've completely lost it."
Svetova's husband Viktor Dzyadko told AFP by telephone that around 10 people took part in the search, which began at 11am (0800 GMT) and lasted some six hours.
Stavitskaya said on Facebook that officers had finished going through the flat and were drawing up an inventory of everything they had confiscated.
She said officers had read documents and downloaded files from computers in the search, which had been sanctioned by a court.
Supporters and friends including novelist Lyudmila Ulitskaya gathered outside Svetova's flat but were not allowed in by investigators.
"She is a rights activist, she is an absolutely honest person who has always worked with prisoners and has done a lot for them," said Ulitskaya.
The 74-year-old novelist added that she remembered witnessing a Soviet-era search of Svetova's father, Felix Svetov, a well-known political dissident.
"We lived through all this once and it seemed that it had ended forever. But evidently it was not forever."