Israel said it bombed Syrian army headquarters in Damascus on Wednesday after warning the Islamist-led government to leave the Druze minority alone in its Sweida heartland.

Syrian government forces entered the majority-Druze city of Sweida on Tuesday with the stated aim of overseeing a ceasefire agreed with Druze community leaders after clashes with local Bedouin tribes left more than 100 people dead.

However, witnesses reported that the government forces joined with the Bedouin in attacking Druze fighters and civilians in a bloody rampage through the city.

The fighting marks the most serious outbreak of violence in Syria since government forces battled Druze fighters in Sweida province and near Damascus in April and May leaving more than 100 people dead.

The Islamist-led authorities have had strained relations with Syria's patchwork of religious and ethnic minorities since they toppled longtime leader Bashar al-Assad in December.

Israeli Defence Minister Israel Katz called on Damascus to "leave the Druze in Sweida alone".

"As we have made clear and warned, Israel will not abandon the Druze in Syria and will enforce the demilitarisation policy we have decided on," he said in a statement.

Syrian forces should withdraw, he added, and promised no let-up in Israeli military attacks until that happened, saying Israel would "raise the level of responses against the regime if the message is not understood".

Shortly afterwards, the Israeli military said it had hit Syria's military headquarters in Damascus.

Syrian state television reported that two people were wounded in central Damascus, without giving a more precise location. (AFP)