The eleven, all former members of the Skorpioni (Scorpions) special police unit, were detained as part of an investigation launched late on Wednesday, a day after local TV stations showed footage of the brutal execution of the six Muslims by Serbian soldiers in Srebrenica almost ten years ago.
The video was used as evidence during the war crimes trials at the International Criminal Tribunal in The Hague.
Aljazeera declined to air parts of the video that showed the executions.
The chief prosecutor of the International Criminal Tribunal for former Yugoslavia (ICTY) Carla del Ponte, currently visiting Belgrade, has welcomed the arrests of the suspects who appeared in the video.
Del Ponte arrived on Friday to Bosnia to meet the country's officials and the top international administrator, British diplomat Paddy Ashdown.
Del Ponte's Balkan trip, which also included visits to Croatia's capital, Zagreb, and Serbia-Montenegro's capital, Belgrade, comes just days before she reports to the UN Security Council on the ex-Yugoslav republics' cooperation with the UN war crimes tribunal.
In Belgrade, she repeated her demands that two most wanted war crimes fugitives - Bosnian Serb wartime leader Radovan Karadzic and his top general, Ratko Mladic - be arrested.
Karadzic and Mladic have been on the run since they were indicted by the tribunal in 1995 for genocide and other war crimes allegedly committed during the 1992-95 Bosnian war, including the 1995 slaughter of as many as 8000 Muslim men and boys at Srebrenica - the worst carnage in Europe since second world war.
Karadzic is believed to be hiding in Bosnia, and Mladic in neighbouring Serbia.