President Volodymyr Zelensky says two people died in Kyiv and another man is killed in Mykolaiv.
Air defence in Ukraine’s capital Kyiv has been engaged in repelling a Russian missile attack, Mayor Vitali Klitschko said, urging citizens to seek shelter.
As Ukraine’s air force warned of cruise missiles heading for the capital, witnesses spoke of hearing explosions.
Air strikes were also reported in the north-eastern Kharkiv region and Cherkasy in the centre, and explosions in Mykolaiv in the south.
In Mykolaiv, one person was injured and taken to hospital, the mayor said.
Others were treated at the scene after the attack which damaged about 20 houses and gas and water supplies, Olexander Senkevych added.
The whole country was put under air alert around 06:00 (04:00 GMT).
According to the Ukrainian air force, Russian cruise missiles were also detected manoeuvring above the western regions of Lviv, Ternopil and Ivano-Frankivsk.
Ukraine has come under frequent air attack since Russia invaded on 24 February 2022, annexing parts of the east and south.