The country observed a day of mourning Monday for victims of the floods in the southern Krasnodar region.
Emergencies Minister Vladimir Puchkov said the warning system failed to operate, RIA Novosti said.
"Mistakes were made by local authorities and certain departments," Puchkov said during a meeting about the floods. "Not all the population was warned in time."
A criminal investigation was under way.
States of emergency were declared in Krymsk, Novorossiysk, and Gelendzhik, where more than 24,000 people were affected by the disaster and more than 640 houses were destroyed, ITAR-Tass reported.
A massive storm struck the region Friday, inundating the area for two days.
As cleanup operations pressed ahead, Russia's opposition lashed out at President Vladimir Putin's government's response to the disaster, RIA Novosti reported.
"This is a direct consequence of the thieving policies carried out by the swindlers and thieves in recent years," opposition leader Sergei Udaltsov said Sunday in St. Petersburg. "Nothing is invested in infrastructure, everything is being stolen."
Putin, who has drawn criticism over his handling of disasters in the 2000s, flew over the Krasnodar region Saturday, RIA Novosti said.
"People were not warned about the powerful floods and their evacuation was not undertaken," Yabloko Party leader Sergei Mitrokhin said on the liberal party's Web site.
Krymsk's emergencies services chief, Denis Pronin, told RIA Novosti residents in the worst-hit town were warned by sirens, text messages and police.
"We did all we could," he said.
Local residents said they weren't warned.
"One of the causes of the catastrophe was the lack of a warning system," Krymsk resident Boris Khovstikov told RIA Novosti. "The civil defense and warning system failed to function."