In January, days after the first-month anniversary of the fall of the Assad regime in a lightning Islamist-led rebel offensive in Syria, a group of young men – some of them armed – were gathered, checking their phones in the nearly empty interior ministry headquarters in Damascus.

With Bashar al-Assad gone, they had arrived from Idlib, a region in the country’s north-west that for years was the only opposition-controlled province in the country.

Virtually overnight, they had been catapulted to positions once controlled by hand-picked Assad supporters and, led by Ahmad al-Sharaa, were in charge of a fractured country devastated by 13 years of civil war.

One of them, around 30 years old, had recently been appointed as a high-profile security official, and welcomed me to a room where any sign of the old regime had been removed. Tall and shy, the official made notes on his iPad while acknowledging that the new rulers faced enormous security challenges, including the threat coming from Assad loyalists.

The dismantling of the decades-old apparatus behind the oppressive machine of the Assads, such as the country’s army and the ruling Baath party, meant the sacking of hundreds of thousands of people.

“There are Assad-affiliated people who haven’t engaged with the reconciliation process,” said the official, who requested anonymity to be able to discuss sensitive issues, citing the new authorities’ call for former members of the security forces to surrender their weapons and ties to the old government.

“Our eyes are on everyone, but we don’t want to give the impression that we’re after them. That’s why there haven’t been massive raids.”

Since then the violence has escalated, particularly in the coastal provinces of Latakia and Tartous, a stronghold of the Assad family, but clashes were relatively contained. Until Thursday.

As forces linked to the government carried out an operation in the countryside of Latakia province, targeting a former Assad official, they were ambushed by gunmen.

At least 13 members of the security forces were killed, according to the Syrian Observatory for Human Rights, a UK-based monitoring group, in what a regional official described as a well-planned attack carried out by “remnants of the Assad militias”.

Initially limited to the Jableh area, the unrest spread more widely. Videos posted online showed heavy gunfire in different areas. The authorities sent reinforcements and, on Friday, further clashes killed more than 120 people, the Syrian Observatory said.

It marked the most violent day since Assad’s fall and the biggest challenge yet to interim President Sharaa’s transitional government and his efforts to consolidate authority.

According to the Institute for the Study of War, a research group, former Assad regime members are likely to form the most effective insurgent cells against Syria’s new rulers with the ability to coordinate attacks.

“[They] already have pre-existing networks that they can leverage to rapidly organize insurgent cells. These networks are military, intelligence, and political networks and criminal syndicates who were regime supporters and lost significant economic and political influence in the aftermath of Assad’s fall,” they said in a report.

Syria’s coastal areas are also the heartland of Assad’s Alawite minority, an offshoot of Shia Islam. Its members held prominent roles in the Assad government but, with the arrival of Sunni Muslim-led rebels, lost the power and privilege they once had. They now say they are under attack and discrimination, despite Sharaa’s pledges to respect different religious sects.

On Friday, activists said gunmen had killed dozens of male residents in Alawite areas, which will further exacerbate tensions – and possibly drive support for insurgents in their anti-government push. The Syrian Observatory said the gunmen were from the government’s security forces, although this has not been verified.

The authorities also faced resistance from the Druze forces in the south, although a deal was reached earlier this week

The government in Damascus does not control the whole of Syria, where different factions – supported by different countries – exercise power over different regions.

But for Sharaa, the challenge goes beyond the task of trying to keep the country safe.

As Western suspicions over his intentions continue, his authorities are also struggling to get crippling sanctions imposed on Syria under the former regime lifted, a vital move to revive the economy of a country where nine in every 10 people are in poverty.