Police said they also confiscated paintings depicting arch-conservative lawmakers and the Moscow patriarch with prison tattoos, Russian news agency RIA Novosti reported.
Alexander Donskoy, owner of the Museum of Power, said Konstantin Altunin's oil-on-canvas portrait showed Putin, the country's president, in a pink-white nightgown touching the hair of Medvedev, the prime minister, who is clad in only a push-up bra and panties.
The painting is part of the gallery's "Rulers" exhibition that opened within the past two weeks, RIA Novosti said.
"Museum property was forcibly seized without any warrants," Donskoy told RIA Novosti. "The rest [of the exhibition] has been sealed, we have no access to it."
Donskoy said police showed up late Monday after a St. Petersburg lawmaker complained.
Police said in a statement posted online the four paintings taken were "withdrawn" because they might "violate existing legislation." It wasn't clear what laws may have been broken, though in Russia it is a crime to insult representatives of authority, the news agency said.