Yury Sydorenko, director of information at Kharkiv city council, said in a statement that Israeli doctors decided after examining his wounds that mayor Gennady Kernes, who is Jewish, could be transported.
"At half past two, he was driven to the airport," Sydorenko added.
The shooting of Kernes in Ukraine's second-largest city was the latest violent incident in the east of the country where authorities have launched what they call an "anti-terrorism" operation against pro-Russian separatists.
Locals officials say he was cycling but his entourage said he was jogging. The city council said he was "hit by a bullet in the back".
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It was not clear whether the attack was directly related to the simmering tensions in eastern Ukraine.
The doctor who performed emergency surgery on him, Valeriy Boyko, said the mayor's life was "in danger".
The mayor is a colourful character, who has a criminal record for theft and fraud and is not known for tolerating dissent.
A one-time supporter of ousted pro-Russia president Viktor Yanukovych, Kernes was known for a particularly robust crackdown on the pro-Western demonstrations that shook Ukraine from November to February, banning any protests to "avoid the spread of infectious diseases".
Pro-Western activists were regularly assaulted. Some had their cars burnt while others were sprayed with a green liquid that is difficult to remove from the skin and impossible to remove from clothes.