The sources said the strike on Gazprom Neft's refinery in southeast Moscow damaged a primary refining facility that accounts for 53 per cent of the plant's capacity.
A second unit is expected to resume operations soon, they said, speaking on condition of anonymity.
Witness footage verified by Reuters showed a fierce blaze and dense black smoke rising from the refinery after the attack.
Local emergency services later said the fire had been put out and had not affected operations - information that was contradicted by the sources, who spoke on condition of anonymity.
Moscow mayor Sergei Sobyanin said a facility at the site had been damaged, without giving further details.
In a separate development highlighting the damage that Ukrainian drone strikes are inflicting, Russian oil producer Tatneft announced country-wide caps on purchases at its fuel stations following an attack on its refinery in Tatarstan last week.
Seeking to hit a major source of Russia's war funds, Ukraine's attacks on refineries have doubled since the start of 2026, leading to full or partial shutdowns of oil processing and a decline in petrol, diesel and jet fuel output, according to official data, social media and Reuters calculations.
The strategy is increasingly straining Russia's domestic fuel market.
A growing number of regions have reported localised supply issues.
The energy ministry sought on Monday to reassure farmers that enough fuel would be available for the critical summer season when they need it for harvesting.
Ukrainian President Volodymyr Zelenskiy said the Moscow refinery was hit from a distance of 500km, illustrating the reach of Ukraine's long-range strikes.
"This is a just response to Russian strikes - and to the dragging out of a war that must be ended," he said on X.
