Minister Murhaf Abu Qasra said all major armed factions had now been integrated into the defence ministry after the new authorities began working to bring them together, but he urged the remaining smaller groups to also join ranks.
"We emphasise the need for the remaining small military groups to join the ministry within a maximum period of 10 days from this announcement," the statement said.
The move was required "to complete the unification and organisation efforts", the statement said, adding "any delay will necessitate taking the appropriate measures according to the law".
It did not identify which groups had not joined the ministry or elaborate on what measures might be taken against any that failed to do so.
Syria's new authorities led by interim President Ahmed al-Sharaa have dissolved the army and security agencies linked to the Assad government.
The new administration also dissolved all armed factions including Sharaa's Hayat Tahrir al-Sham (HTS), which led the lightning offensive that toppled Assad in December.
Factions that agreed to dissolve were integrated into the defence ministry, and General Security, the country's new police, opened the door to recruits as part of both institutions' efforts to create a new army and security force.
Factions from Daraa in the south, as well as Turkey-backed factions in the north and Islamist groups also joined the ministry's forces.
These factions have retained their weapons and remain deployed in their areas of operation.
But HTS and Islamist groups aligned with it remain dominant, especially in their original stronghold in Idlib in the northwest and in Damascus.
Syria's new authorities face major challenges preventing them from asserting control over all of the war-torn country, including the presence of armed groups with varying loyalties.
The main challenge for Abu Qasra, who as a rebel commander led the offensive that overthrew Assad, is building a new national army.
HTS was known as Al-Nusra Front before it broke ties with Al-Qaeda in 2016. Several Western states still proscribe it as a "terrorist" organisation.
On Monday, Syrian Foreign Minister Asaad al-Shaibani warned that postponing implementation of an agreement between Syria's new administration and Kurdish-led forces in the northeast would "prolong the chaos" in the country.
The March deal with the Syrian Democratic Forces (SDF) to integrate the Kurdish administration's civil and military institutions is expected to be implemented by the end of the year.
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