It was the third such incident in two weeks as a US oil embargo stresses the island's grid.
Fuel has been running out across Cuba since January, when US President Donald Trump threatened tariffs on any country that sells or provides oil to the island, deepening the island's ongoing economic and financial crisis.
Public transportation has largely been halted, and officials have cancelled tens of thousands of surgeries.
Cuba produces only 40 per cent of the fuel it needs. A solution for fuel imports is not yet in sight.
The state-owned Electric Union reported that a problem with a generating unit in the eastern province of Holguín caused "a sudden frequency change," resulting in the SEN blackout around midday on Tuesday.
Both the Ministry of Energy and Mines and the Electric Union indicated that "protocols for its restoration have been activated," meaning that "micro-islands" are being established and then interconnected to provide power to priority locations, such as hospitals and food processing plants.
By the afternoon, some parts of the capital Havana had power restored, while authorities indicated that four per cent of the city had electricity.
The provinces of Guantánamo and Cienfuegos reported that they had begun distributing power to their hospitals, and Matanzas confirmed that power had been restored to the city's historic center.
Last week, two nationwide blackouts - on Monday and Friday - left more than nine million Cubans in the dark, adding to two others in March, as well as several regional outages.
The blackouts have a significant impact on the population and, combined with the energy embargo, have led to transportation limitations, reduced work hours and flight cancellations, in addition to serious public health consequences.
The power outages also affect basic activities such as cooking, water supply, and internet and telephone service.
Many families have installed solar backup systems such as panels and portable batteries, and the main mode of transportation for the population consists of electric motorcycles and tricycles equipped with photovoltaic power.
7°C