A Syrian anti-aircraft missile has landed in southern Israel, setting off air raid sirens near the country’s top-secret nuclear reactor, the Israeli military said.

Israel said it responded with an attack on the missile launcher and air-defence systems in neighbouring Syria, but media later described the Syrian missile as an “errant” projectile, not a deliberate attack.

In recent years, Israel has repeatedly launched air strikes at Syria, including at military targets linked to Iran and the Lebanese Hezbollah militia, both allies of Syrian President Bashar Assad.

Such strikes routinely draw Syrian anti-aircraft fire. Thursday’s exchange was unusual because the Syrian projectile landed deep inside Israel.

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Israeli prime minister Benjamin Netanyahu (Debbie Hill/AP)

Syria’s state news agency Sana said the exchange began with an Israeli air strike on Dumeir, a suburb of the capital of Damascus which is believed to house Syrian army installations and batteries as well as bases and weapons depots belonging to Iran-backed militias. Sana said four soldiers were wounded.

The Britain-based Syrian Observatory for Human Rights, an opposition war monitoring group, said the Israeli strikes hit an air defence base belonging to the Syrian military and destroyed air defence batteries in the area. It said the Syrian military fired surface-to-air missiles in response.

Syrian media made no mention of an anti-aircraft missile landing deep inside Israel.

The Israeli military described the projectile that landed near the nuclear site as a surface-to-air missile, which is usually used for air defence against warplanes or other missiles. That could suggest the Syrian missile had targeted Israeli planes but missed and flew off errantly.

However, Dimona, the Negev desert town where Israel’s nuclear reactor is located, is 185 miles south of Damascus, a long range for an errantly fired surface-to-air missile.

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Iranian President Hassan Rouhani, whose country has accused Israel of being behind a series of incidents (Russian Foreign Ministry Press Service/AP)

The Israeli army said it had deployed a missile defence system to intercept the projectile and there had been no damage. The military later said an initial investigation indicated the Syrian missile was not intercepted.

The air raid sirens were sounded in Abu Krinat, a village a few miles from Dimona. Explosions heard across Israel might have been the air defence systems.

Apparent missile fragments were found in a swimming pool in Ashalim, a community approximately 20 miles south west of Dimona. Israeli troops arrived at the scene and collected the fragments.

The military said that in response to the incoming missile, it launched an air strike at the battery that launched the anti-aircraft missile and other surface-to-air batteries in Syria.

The exchange between Israel and Syria comes amid growing tensions between Israel and Iran, a key ally of Syria.

Iran, which maintains troops and proxies in Syria, has accused Israel of a series of attacks on its nuclear facilities, including sabotage at its Natanz nuclear site on April 11, and vowed revenge.

It also threatened to complicate US-led attempts to revive the international nuclear deal with Iran.