The arrival of Nikolic, 48, at the ICTY detention unit in the Scheveningen district of The Hague was confirmed by a tribunal spokesman.
Nikolic, who flew in from Belgrade, was accompanied by Serbian Administration Minister Zoran Loncar, who will provide his government's guarantees for the provisional release of the accused.
Loncar said Nikolic's decision to surrender was brave and responsible.
Nikolic is the ninth war crimes indictee from Serbia and Montenegro to surrender to the ICTY in the last few months, which Loncar said was proof of evident progress in cooperation between Belgrade and the tribunal.
Nikolic, former chief of security in the Bosnian Serb Army Zvornik Brigade, is charged with genocide and complicity in genocide, extermination, murder and persecution in the case of slaughter of more than 7,000 Bosnian Muslim prisoners after Bosnian Serb forces overran the eastern Muslim enclave of Srebrenica on July 11, 1995.
The indictment against Nikolic was issued in September 2002.