He warned Muslim countries not to allow Tel Aviv to create "further trouble for the region".
The two leaders issued a joint statement saying the two sides "discussed ways to advance the Middle East peace process and discussed a number of issues of mutual interest to achieve peace and stability in the Middle East".
Accompanying Netanyahu and his wife, Sara, were National Security Adviser and National Security Council Director Meir Ben-Shabbat; Mossad director Yossi Cohen; the head of the Prime Minister's staff, Yoav Horowitz; the director of the Foreign Ministry, Yuval Rotem; and Brig.
The foreign minister's remarks followed a clandestine visit to Oman by Israeli Prime Minister Netanyahu which came only days after Palestinian President Mahmoud Abbas visited the Gulf monarchy.
Netanyahu's office said he had been invited by the sultan after lengthy communications.
The last Israeli leader to visit Oman was Shimon Peres in 1996.
In August, Benjamin Netanyahu dropped a hint that Israel may join an anti-Iranian Arab coalition in the event Tehran blocks the Bab al-Mandab Strait, the southern entrance to the Red Sea.
Mohammed bin Salman, Saudi Arabia's powerful crown prince, met several Jewish groups and pro-Israel lobbies during a trip to the U.S. earlier this year and declared that Israel had the right to its own land alongside Palestinians.
"Israel is a state present in the region, and we all understand this", bin Alawi said.
In recent years, Netanyahu has insisted that relations between Israel and Gulf countries have been growing, despite none of the seven Gulf states officially recognising Israel.
Mohammed Ali al-Houthi, the president of the Houthi Supreme Revolutionary Committee (SRC), made the remarks in a tweet on Saturday, adding that the real goal of the Israeli premier's trip to Muscat "is to isolate Oman from playing any positive role in the future with its allies and friends".
A trade office in Oman was closed in 2000 during the second Palestinian Intifada.
In another sign of improving relations, Israeli Sports Minister, Miri Regev flew to Abu Dhabi where Israel's judo team was participating in a major tournament.
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