About 50 religious leaders circled over the country on Monday, chanting prayers and blowing the horns called "shofars".
The flight's aim was "to stop the pandemic so people will stop dying from it," Rabbi Yitzhak Batzri was quoted as saying in Yedioth Aharanot newspaper.
The flu is often referred to as H1N1 in Israel, where pigs are seen as unclean.