"Last year, we confirmed 68,000 without specifying the nature of their death and 32,000 this year," civil registries chief Ahmad Rahal said.
He did not provide any additional details about those who had died, including in what part of Syria they had lost their lives or whether they had been victims of the ongoing conflict.
More than 250,000 people killed in Syria war
Thursday's news come after activists accused authorities of quietly updating civil records to mark detainees in regime jails as "deceased" - some backdated by several years.
Human rights defenders say tens of thousands of Syrians are held in government jails across the country.
Relatives and advocates say they are often tortured, denied a fair trial, and deprived of contact with their families.
But Rahal said employees at the civil record did not have a "missing" box to tick.
"If a document comes through from any government body - whether a hospital or another - to confirm a death, it is confirmed without specifying if they were missing or not."
The Syrian Network for Human Rights has documented around 400 cases in recent months, including those of nine children, where civil registry employees have told family members that their detained relative has died.
More than 350,000 dead: Syria's war in numbers
There could be further such instances which are yet to be documented.
Around 80,000 remain forcibly disappeared by the government, the rights group says.
More than 350,000 people have been killed since Syria's civil war started in 2011, the Britain-based Syrian Observatory for Human Rights monitor says.
More than 33,000 were killed last year alone, including more than 10,000 civilians and 7,000 pro-regime fighters, it says.
During the first seven months of this year, at least 14,000 people lost their lives among them more than 5,000 civilians and 7,000 soldiers and loyalists.
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