The Knesset's Ethics Committee voted to suspend Hanin Zoabi from most parliamentary debates until the summer recess early next month, while allowing her to take part in any votes held in the current session.
Zoabi was punished after three lawmakers filed complaints against her for travelling aboard the Mavi Marmara, a converted cruise ship stormed by the Israeli navy as it led a six-vessel pro-Palestinian flotilla towards Gaza in May 2010. Nine Turkish activists on the ship were killed in fighting with marines.
The ethics committee said in a statement that Zoabi had "participated in an action destined to threaten state security."
It accused her of cooperating with the Turkish charity IHH, which provided funds and volunteers for the Mavi Marmara mission and is outlawed in Israel because of its links to Hamas, an Islamist group hostile to the Jewish state.
Zoabi, who has denied wrongdoing in the flotilla incident and says she tried to mediate between the activists and Israeli forces, cried foul at Monday's decision.
"An automatic right-wing majority should not be permitted to punish me for my political views," she told Israel's Army Radio.
Zoabi, 42, the only female member of parliament in a party representing Israel's 20 percent Arab minority, is a vociferous critic of the conservative government's Palestinian policies. She was stripped of some of her diplomatic privileges by the Knesset last year.
One of 13 Arab lawmakers in the 120-seat Knesset, Zoabi's party calls for Israel to stop being a Jewish state and redefine itself as a multi-ethnic country.
Most Israeli Arabs are descended from Palestinians who remained during the 1948 war when the state was founded, while hundreds of thousands of others fled or were driven out.
Though guaranteed full civic rights, many Israeli Arabs complain of suffering discrimination under the Jewish majority.
Israel says it keeps Gaza under naval blockade because it fears Hamas could smuggle in arms. But the global outrage caused by its seizure of the ship on the high seas last year has prompted it to allow limited trade through the land borders of the enclave, most of whose 1.5 million Palestinian population depend on aid to survive.