"I don't agree either with slogans nor statements made at the rallies. All the same I have issued orders to probe all the information concerning the observance of electoral law at the polling stations," Medvedev wrote on his Facebook status.
Calling for fair elections in the wake of last weekend's parliamentary polls, allegedly rigged in favour of the ruling Russia United party of Putin, some 50,000 Russians on Saturday took to the streets demanding an end to Putin's 'managed democracy'.
Commenting on yesterday's protest rallies, largest of which was held at Bolotnya Square near the Kremlin, Medvedev noted that under the Russian constitution the people have freedom of speech and gathering in public.
"People have right to express their views, which they did on Saturday. Its good that everything proceeded within the framework of law," Medvedev wrote in his Facebook blog.
The protests come three months before the Russian strongman, who was president in 2000-2008 and effectively remained incharge of the country's while prime minister, will seek a third presidential term.
Last Sunday's Parliamentary election for lower house Duma signalled the end of Putin's honeymoon with Russia. Putin's 'United Russia' lost its overwhelming majority of 315 seats in the 450-strong lower house, but retained 238 seats allegedly due to mass-scale ballot rigging.
Facing rare street demonstrations against his rule, Putin on Tueseday accused the US of instigating post-election protests in Russia that are posing a challenge to his authority.