Wuhan officials attributed the new figure to updated reporting and deaths outside hospitals. China has insisted there was no cover-up.
It has been accused of downplaying the severity of its virus outbreak.
Wuhan's 11 million residents spent months in strict lockdown conditions, which have only recently been eased.
The latest official figures bring the death toll in the city in China's central Hubei province to 3,869, increasing the national total to more than 4,600.
China has confirmed nearly 84,000 coronavirus infections, the seventh-highest globally, according to Johns Hopkins University data.
The virus has had a huge impact on the Chinese economy, which shrank for the first time in decades in the first quarter of the year.
In a statement released on Friday, officials in Wuhan said the revised figures were the result of new data received from multiple sources, including records kept by funeral homes and prisons.
The "statistical verification" followed efforts by authorities to "ensure that information on the city's Covid-19 epidemic is open, transparent and the data [is] accurate", the statement said.
It added that health systems were initially overwhelmed and cases were "mistakenly reported" - in some instances counted more than once and in others missed entirely.
A shortage of testing capacity in the early stages meant that many infected patients were not accounted for, it said.
A spokesman for China's National Health Commission, Mi Feng, said the new death count came from a "comprehensive review" of epidemic data.
In its daily news conference, the foreign ministry said accusations of a cover-up, which have been made most stridently on the world stage by US President Donald Trump, were unsubstantiated. "We'll never allow any concealment," a spokesman said.