Avaaz.org said its investigation has identified 2,918 Syrians who were arrested or abducted by security troops and whose whereabouts are now unknown.
"Hour by hour, peaceful protesters are plucked from crowds by Syria's infamously brutal security forces, never to be seen again," said Ricken Patel, executive director at Avaaz.
The group called on the international community to step up demands for the release of the disappeared and for a transition to democracy in Syria.
Syrian activists say more than 1,600 people – most of them unarmed protesters – have been killed by security forces since the revolt against Assad's rule erupted in mid-March.
Although the uprising began with calls for reform, the steadily climbing death toll and slow pace of reform has enraged the protesters' movement. Now, many of them say they won't accept anything short of Mr Assad's ouster.