The 7-6 vote against the deal by the Knesset's economics committee was however non-binding and Netanyahu is expected to seek to move ahead anyway, with a court battle likely to result.
Committee spokesman Lior Rotem told AFP the vote was against Netanyahu's plan to bypass usual antitrust oversight, on the grounds of diplomatic and security needs.
"It's a recommendation," he said. "The government is not obliged to accept this recommendation."
Thousands have staged street protests against the agreement which they said amounted to a "gift" for the consortium.
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The deal had already been approved by the government, but opponents are expected to challenge its legality in the Israeli High Court.
Israel has been trying to extract offshore gas since the discovery of the Tamar and Leviathan fields in 2009 and 2010.
While extraction has begun in Tamar, the far larger Leviathan has been hit by a series of delays.
To sidestep its objections, Netanyahu wants to use an obscure clause allowing the deal to be pushed through by order of the economy minister - a portfolio currently held by him, along with foreign affairs and other posts.
For resource-poor Israel, the aim is to use the gas to become more economically independent, lower energy prices and potentially export its gas.
Neighbouring Egypt recently discovered what was described as the "largest ever" gas field in the Mediterranean, sparking fears in Israel that the country could fall behind.
The size of the Leviathan field is estimated at 18.9 trillion cubic feet (535 billion cubic metres, or bcm) of natural gas, along with 34.1 million barrels of condensate.
Noble and Delek also control the Tamar field, which holds 250 bcm of natural gas, and lies 80 kilometres (40 nautical miles) west of the northern Israeli port city of Haifa.