Mykhailo Podoliak, an advisor to Ukraine's President Volodymyr Zelensky, linked in a tweet on Sunday Iran's support for Russia's invasion of his country with the night-time strike on a military site.
"Explosive night in Iran -- drone and missile production, oil refineries," he said. "War logic... bills the authors and accomplices strictly".
"Ukraine did warn you," Podoliak added.
Iran's foreign ministry said Ukraine's charge d'affaires in Tehran had been summoned to provide "an official and immediate explanation from the Ukrainian government".
It called Podoliak's remarks "strange and biased", adding in a statement it hoped "such positions will not be repeated".
Iranian authorities reported an "unsuccessful" drone attack late Saturday night that targeted a defence ministry "workshop complex" in the central Isfahan province, home to the Natanz nuclear enrichment facility.
An anti-aircraft system destroyed one drone and two others exploded, the defence ministry said, adding that there were no casualties and only minor damage to the site.
Dramatic video footage widely shared on social media and published by Iranian state media showed a fireball lighting up the night sky, with people outside seen running and emergency service vehicles speeding towards the site.
Ukraine and its Western allies have accused Iran of supplying military drones to Russia for its war in Ukraine, a claim that is denied by Tehran.
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