Putin told at a news conference on Monday that Ukrainian drones had used the same marine corridors that grain ships transited under the UN-brokered deal.
Kyiv has not claimed responsibility for the attack and denies using the grain programme's security corridor for military purposes.
The United Nations said no grain ships were using the Black Sea route on Saturday when Russia claimed its vessels in Crimea were attacked.
Meanwhile, Russian missiles rained down across Ukraine, with explosions blooming out in Kyiv, sending black smoke into the sky.
Russian forces shelled infrastructure in at least six Ukrainian regions on Monday, the general staff of the Ukrainian Armed Forces said on Facebook.
"That's not all we could have done," Putin said at the televised news conference.
Ukrainian officials said energy infrastructure, including hydroelectric dams, was hit knocking out power, heat and water supplies.
Oleh Synehubov, governor of the northeastern Kharkiv region, said on Telegram that about 140,000 residents were without power after the attacks, including about 50,000 residents of Kharkiv city, the second-largest city in Ukraine.
Ukraine's military said it had shot down 44 of 50 Russian missiles. But strikes left 80% of Kyiv without running water, authorities said. Ukrainian police said 13 people were injured in the latest attacks.
For the past three weeks, Russia has attacked Ukraine’s civil infrastructure using long-range missiles and suicide drones that fly at a target and detonate.
Ukraine's Prime Minister Denys Shmyhal said 18 targets, mostly energy infrastructure, were hit in missile and drone strikes on 10 Ukrainian regions on Monday.
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