Ukraine was contracted to buy 2 billion cubic meters of gas from Russia in February for a total of $720 million. However, it bought only half that volume.
"Ukraine is currently not buying the volume of gas from us that it was contracted to do, and should pay a fine for this. We are waiving this fine, based on realities - they can't pay. They are now on the verge of bankruptcy," Putin said, at a meeting with miners in Siberia.
Alexei Miller, the CEO of Russian gas giant Gazprom, said earlier this month that Gazprom was not seeking fines from Ukraine over the fall in gas imports.
Ukraine has asked Russia for a $5 billion loan to pay for gas deliveries.
Gazprom temporarily suspended gas deliveries to Ukraine at the start of the year over a payment delay, and the sides' failure to reach a new gas deal.
Earlier this week, Putin said that a recent dispute surrounding Ukrainian national energy company Naftogaz, "discredited" the country, and could lead to Russia seeking alternative routes for gas transit to Europe.