It was a sudden escalation in pressure on the opposition, but tensions already were running high.
Putin has taken a harder line against the opposition since returning to the presidency in May, seemingly no longer willing to tolerate the peaceful protests that drew tens of thousands of people onto the streets of Moscow ahead of the March election that handed him a third term.
A measure Putin signed into law on Friday will raise fines on those who take part in unauthorized protests 150-fold, to nearly the average annual salary in Russia. Tuesday's protest has city approval, but any actions that violate the agreed upon location and timeframe could give police a pretext to make arrests.
The top Twitter hashtag in Russia on Monday was "Welcome to the Year '37," a reference to the height of the purges under Soviet dictator Josef Stalin.
Opposition activists predict the government crackdown on dissent and the anger it has fueled will bring out more protesters on Tuesday, a patriotic holiday called Russia Day. The holiday marks the day in 1990 when Russian lawmakers declared independence from the Soviet Union by giving supremacy to Russian laws over Soviet legislation.
The Kremlin, however, appears to be betting that the tough measures will frighten away the young white-collar professionals whose new political activism has posed the first serious challenge to Putin since he came to power in 2000.
State Department spokeswoman Victoria Nuland said the U.S. is "deeply concerned by the apparent harassment of Russian political opposition figures on the eve of the planned demonstrations on June 12."
"Taken together, these measures raise serious questions about the arbitrary use of law enforcement to stifle free speech and free assembly," she told reporters in Washington.
A spokesman for the investigators, Vladimir Markin, confirmed that the apartments searched Monday included those of Alexei Navalny, Sergei Udaltsov, Ilya Yashin and also of television personality Ksenia Sobchak, whose father was Putin's mentor.
Udaltsov said on Twitter that investigators had turned his apartment upside down and taken away computers, sacks of papers and the flags of his leftist movement.
Navalny tweeted the arrival of the investigators, but later went silent as the search dragged on for 12 hours. His spokeswoman Anna Veduta, who said he called her from his home phone, tweeted that investigators had seized his cell phones, tablet and computer. Investigators eventually emerged carrying boxes of material seized from Navalny's apartment.
The homes of Udaltsov's parents and Navalny's parents and in-laws also were searched, the opposition leaders said.
Markin said that investigators, working with city police, also planned to search the apartment of veteran opposition leader Boris Nemtsov.
The spokesman said all of the opposition leaders subject to searches had been summoned for questioning on Tuesday as part of an investigation into the last big opposition rally on May 6, the day before Putin's inauguration, which turned violent after police restricted access to the square where the rally was to be held. Bottles and pieces of asphalt were hurled at police, who struck back by beating protesters with truncheons and detaining more than 400.
A lawyer representing the opposition, Nikolai Polozov, said it was possible the protest leaders could find themselves under arrest, the Interfax news agency reported.
They have been summoned for questioning at 11 a.m., just an hour before protesters are to begin gathering on Pushkin Square. The protesters are to march along the boulevard that circles central Moscow toward Sakharov Avenue, where a rally is to be held from 3 p.m. to 6 p.m.
If the demonstration ends peacefully and as planned, police should have no cause to intervene. But if some of the protesters set off on a new march, as some have suggested they may do if the opposition leaders are still being held for questioning, police would have the right to make arrests and the penalties would be harsh. The opposition has also warned of the dangers of provocations by pro-Kremlin forces hoping to set off clashes between protesters and police.