Damascus is capable of deterring Israel but will practice restraint, Syria's Foreign Minister Faruq al-Shara said in a letter to the United Nations on Sunday.
The Israelis had earlier claimed that it attacked an Islamic Jihad and Hamas training base in the Ain al-Sahab area, about 20km northwest of Damascus.
It did not say whether air or ground forces carried out the strike, but an unnamed security source was quoted as saying that it was an air attack early on Sunday.
Both the Islamic Jihad and Syrian sources have denied that the area housed a training base.
"Jihad has no combatants outside the Palestinian territories," the group's Beirut-based spokesman Abu Imad Rifai told Aljazeera.
Syrian analyst Dr Imad Shuaibi said the attack was aimed at sparking chaos in the region and send a message to Damascus that Israel was willing to take military action.
Shuaibi said the area housed refugees.
Islamic Jihad insists its activists in Syria are part of the group's media bureau.
Several civilians were injured in the strike, said a Lebanon-based official for Popular Front for the Liberation of Palestine-General Command (PFLP-GC).
"The significance of the operation is more in terms of its symbolic message to the Syrians... It simply says that nobody is immune"
a retired senior Israeli military
The attack is believed to be the first Israeli strike deep into Syrian territory since the 1973 Arab-Israeli war. It took place on the eve of that war's 30th anniversary.
An anonymous source said the attack targeted "an abandoned training camp" that belonged to the Popular Front for the Liberation of Palestine (PFLP).
Israel could launch more attacks in Syria if it continues to support what they said were "terrorist organisations" preparing anti-Israeli attacks, according to Israeli Prime Minister Ariel Sharon's spokesman.
Hamas and Islamic Jihad are spearheading the three-year-old Palestinian Intifada against Israel's occupation.
Syria said it would complain to the UN Security Council. It also plans to ask the 15-member body to hold a special session to discuss the attacks, according to an unnamed diplomatic source.
Damascus is a member of the Security Council, but does not hold veto power.
Egypt's President Husni Mubarak condemned the strike, calling it an aggression against a "brother country".
Mubarak was speaking at a press conference in Cairo with visiting German Chancellor Gerhard Schroeder.
For his part, Schroeder said the attack "cannot be accepted". The German Chancellor said regional peace efforts "become more complicated when...the sovereignty of a country is violated".
The Israeli army said the attack was in response to Saturday's blast in the northern Israeli city of Haifa that killed about 19 people. The Islamic Jihad claimed responsibility for the blast.
In the occupied Gaza Strip, Israel launched two helicopter attacks on the homes of resistance fighters.
Helicopter gunships fired several missiles at al-Buraij refugee camp, shortly after 1am local time (23:00 GMT) on Sunday.
Israel released footage claiming
to show targeted camp in Syria
Witnesses said the target was the house of an Islamic Jihad activist, which was empty at the time. Israeli public radio said the target was an arms and explosives dump.
The attack came shortly after a similar strike on the Gaza City home of another resistance fighter, which left several people injured by flying glass.
Palestinian security sources identified him as Munthir Qanita, a member of the armed wing of the Islamist resistance group Hamas. His home was also reportedly empty at the time of the attack.
The two Israeli missile attacks were an apparent reprisal for a bombing in Haifa in which a Palestinian woman from the occupied West Bank town of Jenin blew herself up and killed 19 others in a restaurant in the northern Israeli city.
Islamic Jihad claimed responsibility for the attack which followed continuing Israeli raids and killings in the Palestinian territories.
Israeli forces demolished the home of the bomber, Hanadi Jaradat, in the occupied West Bank city of Jenin during a dawn invasion.
Activists from the International Solidarity Movement (ISM) tried to prevent occupation troops from destroying the house and were beaten by Israeli forces, reported our correspondent in Jenin.
Dozens of tanks stormed the city, as Israeli slapped a curfew on the population.
Fears for Arafat
Arafat's fate unclear after Haifa
bombing and Israeli threats
Following the Haifa blast, Israel said the clock is ticking for Palestinian President Yasir Arafat.
An Israeli warplane was seen hovering over Arafat's Ram Allah compound in the occupied West Bank.
About 30 foreign and Israeli peace activists joined others at his headquarters in the West Bank town of Ram Allah to act as human shields.
The Israeli human shields reportedly include at least one former member of the Israeli parliament.
Clashes broke out in Ram Allah on Saturday night as deployed Israeli troops were confronted by stone-throwing Palestinian residents.
The Haifa bombing has renewed calls for Israel to carry out its decision to kill or remove Arafat.