The Investigative Committee said anti-corruption campaigner Alexei Navalny and leftist radical Sergei Udaltsov -- both sentenced on Wednesday to 15 days' detention for a different protest -- would soon be questioned.
Navalny's attorney Vadim Kobzev tweeted that his client had already been transferred from his Moscow detention centre to the committee for the interrogation. Interfax reported that Udaltsov had also been moved.
Moscow police said they detained more than 400 protesters Sunday during a "March of Millions" that leaders of Russia's nascent protest movement staged ahead of Putin's swearing in to an historic third presidential term.
The Investigative Committee said more than 30 police were wounded in bloody scuffles with demonstrators that broke out across the Moscow River from the Kremlin as protester numbers swelled into the tens of thousands.
Navalny and Udaltsov had ordered supporters to stage a sit-down strike in the middle of the march and then refused police orders to keep on moving.
The protest movement's two most prominent leaders risk being charged with calling for mass insubordination and using force against police. The latter offence carries a maximum 10-year prison term if police are injured.
The 35-year-old Navalny is a lawyer by training who gained celebrity status among Russian bloggers for waging an Internet campaign to expose state corruption and sweetheart government deals.
He has refused to rule out one day running for the Russian presidency.
Surveys show his recognition level rising quickly and analysts identify him as an emerging political threat for Putin as he extends his 12-year domination of Russia through to at least 2018.
The shaven-headed Udaltsov enjoys support from Russia's far-left and the Communist Party as well as from some members of the A Just Russia parliamentary opposition party.