David Gilo expressed his opposition to the dominant position of US giant Noble Energy and its Israeli partner Delek to exploit gas from the Leviathan and Tamar offshore gas fields in the letter sent to Economy Minister Arye Deri.
But Netanyahu said in a statement that Gilo was alone to have opposed the set-up.
"This set-up increases competition, guarantees the extraction of gas... Attracts new investors... And promotes important national interests by providing gas to several countries in the region," he said
Gilo's resignation, due to take effect in August, saw Delek's share price immediately rise by more than three percent during today trading on the Tel Aviv Stock Exchange.
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In his letter, Gilo wrote that preserving the stranglehold of Noble and Delek on the natural gas market "undermines competition, and the power of authority" of the Antitrust Authority.
The watchdog moved late last year to scrap the deal that gave the two firms control over Leviathan, at the time classifying their partnership as a "cartel".
Noble and Delek also control the Tamar field, which holds 250 bcm of natural gas, and lies 80 kilometres (43 nautical miles) west of the northern Israeli port city of Haifa.