HRW said those targeted by the regime included former opposition activists and rebel fighters as well as their family members.
The Syrian regime has carried out a wave of arbitrary arrests against former activists in rebel areas who surrendered under deals brokered by its ally Moscow, Human Rights Watch said on Tuesday.
The so-called "reconciliation" agreements that restored regime control over swathes of central and southern Syria last year were heavily criticised from the start because they were signed under the pressure of military blockade and intense air and artillery bombardment.
The regime offered amnesty to all who agreed to end their anti-regime activities.
But thousands of residents, particularly former fighters and their families, chose to be evacuated to camps in remaining rebel-held territory rather than accept renewed rule by Bashar al Assad's regime.
Human Rights Watch said its research showed that former regime critics and rebels who signed up for "reconciliation" had paid heavily for their decision.
It said it had documented 11 cases of arbitrary detention and disappearance in three areas retaken by regime forces last year – the southern province of Daraa, the Eastern Ghouta suburbs of Damascus and southern neighbourhoods of the capital.
Syrian organisations had documented at least 500 arrests in the three areas since August, it added.
"Active combat has ended in much of Syria, but nothing has changed in the way intelligence branches trample rights of perceived opponents of Assad's rule," said HRW's acting Middle East director, Lama Fakih.
"Lack of due process, arbitrary arrests, and harassment, even in so-called reconciled areas, speak louder than empty regime promises of return, reform and reconciliation."
HRW said those targeted included family members as well former opposition activists and rebel fighters.
"In all cases, the people targeted... had signed reconciliation agreements with the regime," it said.
It called on Moscow to use its influence with its Damascus ally "to stop arbitrary detention and harassment," and help "release arbitrarily held detainees."