Civilians, including two women, were among those killed in "the deadliest Israeli attack in the Syrian capital" so far, said Rami Abdel Rahman, head of the Syrian Observatory for Human Rights.

The overnight strike damaged a 10-storey building near an Iranian cultural centre in the capital's Kafr Sousa district, which is home to senior state officials and Syrian intelligence headquarters, said the Britain-based Observatory.

It was not immediately clear who was the intended target of the strike which AFP correspondents reported left a large crater in the rubble-strewn street below and blew out windows of nearby buildings.

Other missiles overnight hit a warehouse that belongs to pro-regime Iranian and Hezbollah fighters near Damascus, said the Observatory, which relies on a wide network of sources inside Syria.

Syria's defence ministry confirmed the Kafr Sousa attack shortly after midnight and gave an initial death toll of five, including one soldier, and 15 wounded civilians, some of whom it said were in critical condition.

"At 00:22 am, the Israeli enemy carried out an aerial aggression from the direction of the occupied Golan Heights targeting several areas in Damascus and its vicinity, including residential neighbourhoods," it said.

Syrian defence forces had "shot down several missiles", the ministry added in its statement.

An Israeli army spokesperson on Sunday said only that "Israel does no comment on reports in foreign media".

- More than decade of war -

Israel, during more than a decade of war in Syria, has carried out hundreds of air strikes against its neighbour, primarily targeting the country's army, Iranian forces and Hezbollah, allies of the Damascus regime.

Israel's military rarely comments on its operations inside Syria, but regularly asserts that it will not let its arch enemy Iran extend its influence to Israel's borders.

Late last year, the head of the Israel Defense Forces Operations Directorate, Major General Oded Basiuk, presenting an operational outlook for 2023, said that the army "will not accept Hezbollah 2.0 in Syria".

In Tehran, foreign ministry spokesman Nasser Kanani on Sunday "strongly condemned the attacks of the Zionist regime against targets in Damascus and its suburbs, including against certain residential buildings".

The raids had left "a number of innocent Syrian citizens" dead and injured, he said.

The Syrian conflict started in 2011 with the brutal repression of peaceful protests, and escalated to pull in multiple foreign powers and global jihadists.

Nearly half a million people have been killed, and the conflict has forced around half of the country's pre-war population from their homes.

The Syrian regime of President Bashar al-Assad receives military support from Russia as well as from Iran and Tehran-allied armed Shiite groups, including Lebanon's Hezbollah, which are declared enemies of Israel.

The latest attack comes more than a month after an Israeli missile strike hit Damascus International Airport, killing four people, including two soldiers.

The January 2 strike hit positions of Hezbollah and pro-Iranian groups inside the airport and nearby, including a weapons warehouse, the Observatory said at the time.

The Damascus government is currently seeking to recover from the February 6 earthquake, which did not affect the capital but which killed more than 43,000 people across the country's north and southern Turkey.