The date of Boskoski's first court appearance has not been set yet.
He arrived in Amesterdam this morning escorted by an employee of Interpol Croatia.
The 44-year-old Boskoski was Macedonia's interior minister from May 2001 to November 2002. Until his transfer to The Hague he was detained in Pula, Croatia, for the killing of seven Asian immigrants by police on the Macedonian border in 2002.
Boskoski has dual Macedonian and Croatian citizenship.
When he was read the Hague tribunal's indictment in Pula, he pleaded not guilty. He said he recognised the legitimacy of the UN court and that he would surrender.
The Hague tribunal has charged him with three counts of violations of the laws and customs of war due to a police attack on Ljuboten, a village near Skopje, in August 2001. Seven Albanians were killed, about 100 were detained and mistreated, while about 30 houses and other buildings were set on fire or destroyed.
Boskoski has been indicted alongside Johan Tarculovski, 30, the Interior Ministry officer who led the attack. He has been in detention in The Hague since March 17.
The indictment against Boskoski and Tarculovski is the last issued by the International Criminal Tribunal for the former Yugoslavia.