Police are searching for one suspected perpetrator, news agency TT reported.
Swedish Justice Minister Gunnar Strommer said the Justice Ministry was in close contact with the police and that it was closely monitoring developments in the case.
"A brutal act of violence has occurred in central Uppsala ... This is at the same time as the whole of Uppsala has begun Walpurgis Night. What has happened is extremely serious," Strommer said in a statement.
Police said earlier they had received calls from members of the public who heard gunshots in the city centre, and that emergency services had rushed to the scene.
"Three people are confirmed dead after a shooting ... The police are investigating the incident as a homicide," investigators said in a statement.
Witnesses told SVT they had heard five shots and had seen people in the area running to take cover. Several Swedish media, including TT, reported that the shooting took place near or in a hair salon.
Ten people were killed in February in the Swedish city of Orebro in the country's deadliest ever mass shooting, in which a 35-year-old unemployed loner opened fire on students and teachers at an adult education centre.
Sweden has suffered from a wave of gang-related violence for more than a decade that has included an epidemic of gun violence.
The Nordic country's right-wing minority government came to power in 2022 on a promise to tackle gang-related violence. It has tightened laws and given more powers to police, and after the Orebro shooting said it would seek to tighten gun laws.
(Reporting by Louise Breusch Rasmussen and Stine Jacobsen in Copenhagen, Johan Ahlander, Marie Mannes, Simon Johnson and Niklas Pollard in Stockholm and Philip O'Connor in Uppsala, editing by Terje Solsvik, Gareth Jones and Sandra Maler)

epaselect epa12063221 Police at the scene after a shooting at Vaksala Square in Uppsala, Sweden, 29 April 2025. According to police, three people were confirmed dead after a shooting which is being investigated as a murder. EPA-EFE/FREDRIK SANDBERG SWEDEN OUT