Cupet blames the deficit on logistical difficulties and higher-than-usual demand.
Cuba is facing its second fuel shortage in seven months, authorities have said, as long lines snaked around many Havana filling stations.
Thursday's queues came a day after state-run Cuba-Petroleum Union (Cupet) announced "a deficit in the availability of fuel" and delivery "difficulties."
"If you manage to find gasoline, then you can waste a whole lot of time waiting in line. Because the queues can go around the whole block," Michael Sanchez, a young driver who waited 10 hours to put gas in his car in Havana, told the AFP news agency.
Cupet blamed the deficit on logistical difficulties and higher-than-usual demand, in a statement published on Twitter on Wednesday.
Communist-led Cuba, which is facing its worst economic crisis in almost 30 years due to the effects of the Covid-19 pandemic and US sanctions, had similar problems in March.
The current distribution crisis comes almost three months after a major fire at a storage plant in the province of Matanzas, which left 17 dead, destroyed four mega-tanks of crude oil and caused $100 million in losses just for the fuel burned, according to official data.
READ MORE: Cuba without power after Hurricane Ian destroys electrical grid
Caught between Russia and US
At a time when Cuba is urging the Biden administration to ease US sanctions that it says stifle hurricane recovery efforts, Russian oil has flooded into the island, providing relief to debilitating blackouts.
Russia has shipped an estimated $352 million in oil to Cuba since the start of the Ukraine war, the biggest inflow from Russia this century and enough to cover about 40 percent of the shortfall in the island's supplies, according to independent estimates.
The sales also potentially alleviated the weight of international sanctions on Russia for its incursion on Ukraine.
In an increasingly complex geopolitical situation, the island nation has been left with its hands tied.
"(It leaves them) between a rock and a hard place," said William LeoGrande, a professor at American University who has tracked Cuba for years.
"Cuba can’t afford to alienate either side in what is shaping up to be a new Cold War."
Cuba has depended on foreign oil as its primary energy source for decades.
Until the fall of the Soviet Union in 1991, the Soviets sold Cuba oil well below market price. Later, Cuba hatched a similar deal with socialist ally Venezuela at the height of its oil boom, sending Cuban medics in exchange for discounted petroleum.
Since Venezuela has fallen into its own crisis, though, Cuba has been left short on both oil and a way to pay for it.
READ MORE: Ukraine-Russia conflict: Can we learn from the Cuban Missile Crisis?
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