Israel on Monday inaugurated with its US ally a joint missile defence base on Israeli soil, the first ever, a senior Israeli air force officer said.

The new facility, at an undisclosed location in southern Israel, was announced as Israeli Prime Minister Benjamin Netanyahu was due to meet US President Donald Trump in New York on the fringes of the UN General Assembly.

"We inaugurated, with our partners from the United States Army, an American base, for the first time in Israel," Brigadier General Tzvika Heimowitz, head of Israeli missile defences, told journalists.

"An American flag is flying permanently over a US army base situated inside one of our bases."

Heimowitz said the move was not a direct response to any specific incident or immediate threat, but was a combination of "lessons learned" in the 2014 war in Gaza and intelligence analysis of future dangers.

"We have many enemies around us, near and far," he said.

The outgoing Israel air force chief in June warned neighbours of the "unimaginable" military power at the country's disposal.

On September 7 Syria's army accused Israeli warplanes of hitting one of its positions, killing two people in an attack that a monitor said targeted a site where the regime allegedly produces chemical weapons.

Israel, without confirming it was behind the attack, indirectly warned Syria and Iran that it would not tolerate any "Shiite corridor from Tehran to Damascus".

Israel accuses Iran of building sites to produce "precision-guided missiles" in both Syria and Lebanon and Netanyahu is expected to reiterate the point in his talks with Trump.

The country has bought 50 F-35 stealth fighters from the United States.

Israel has a sophisticated anti-missile defence system, including the Iron Dome short-range interceptor which has successfully brought down rockets fired from Syria, Lebanon, Egypt's lawless Sinai region and the Gaza Strip.

It also has the medium-range David's Sling and the Arrow missile defence system, designed to counter more distant threats.

Heimowitz did not comment on the specific role of the new joint base, but said the "few dozen" US personnel there would be under Israeli command.

"This is not part of an exercise or manoeuvre," he said. "It is a presence as part of the joint effort of Israel and the US to improve defence."

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