The fatalities were unvaccinated and aged between 89 and 91 with underlying diseases, officials said.
China is battling its worst outbreak since the beginning of the pandemic in 2020 and has imposed one of the biggest lockdowns in its biggest city, prompting public anger.
The city of more than 24 million people has recorded at least 320,000 infections since March, but no Covid deaths were attributed to it – a claim that has come under scrutiny with local media reporting the number of deaths of people in care homes.
But authorities have attributed these deaths to underlying health problems.
In a statement announcing the deaths, Shanghai’s Health Commission said that the three people’s condition grew worse after entering the hospital and they died despite “full efforts to resuscitate them”.
In Shanghai, only 62 per cent of residents over 60 were fully vaccinated, according to officials.
The city has been reporting more than 20,000 cases daily, with 22,248 cases detected on Sunday.
Residents are now expecting another round of mass testing imminently, meaning the strict lockdown will run into a fourth week.
Authorities in China which is following a “zero-Covid” strategy said they will consider the outbreak is contained when there are no new infections outside quarantined buildings or areas.
Under the lockdown, millions of people have been confined to their homes and those testing positive, having few or no symptoms, are being sent to quarantine centres. This has led to widespread unrest among residents, with reports of people clashing with police for forcing them into quarantine facilities.
There have been complaints of shortages of food and other daily necessities, while tens of thousands of people put under medical observation have been sequestered in crowded facilities where lights are always on, rubbish bins overflow, food is inadequate and hot showers nonexistent.
Struggling with a rising number of cases, the city has converted exhibition halls and schools into quarantine centres and is setting up makeshift hospitals.
The lockdowns have exacerbated the country’s economic growth which is still weak at 4.8 per cent over a year earlier in the first three months of 2022 as lockdowns cut production in major industrial cities. Official data showed growth accelerated from the previous quarter’s 4 per cent.
On Monday, Vice Premier Liu He, President Xi Jinping’s top economic adviser, pledged to increase spending to stabilise supply chains and provide financial support for health workers and others on the pandemic front lines.
Additional reporting by agencies