"I ordered to stop the vaccinations until things are made clear," Yacov Ben Yizri, the Israeli health minister, said on Sunday.
"We have started to investigate everything related to this case," he said.
The ministry said it had asked the French firm Aventis, which manufactured the vaccine, to conduct its own investigation.
Three of the four men who died had been vaccinated at the same medical centre and injected from the same vaccine pool.
One died hours after receiving the vaccination on Thursday.
Three died from cardiac arrest and the immediate cause of death of the fourth is unknown.
Hospital officials said they were aged 52 to 76 and had suffered from ailments including diabetes and heart disease.
People aged 65 or older or those with severe heart conditions are at high risk from complications from influenza, which kills hundreds of thousands of people worldwide each year, and are usually encouraged to be vaccinated against it.
Ben Yizri said more than 140,000 people had been vaccinated for the flu virus in Israel this year.
The risk of death from such a vaccine, which contains an inactivated virus, is small.