"The commercial supply of gas began today after two days of testing," said spokesman Zeev Feiner, CNN reported Saturday.
The pipeline, which also routes Egyptian gas to Syria, Jordan and Lebanon, has been sabotaged twice since February, when former Egyptian President Hosni Mubarak resigned.
In Egypt and Israel, the pipeline has been controversial with some accusing the Egyptian government and Israel of negotiating cheaper-than-market-value prices for the natural gas.
Both sides deny any impropriety.
The Merhav group of companies is a major shareholder in the pipeline that is managed by the East Mediterranean Gas Co.