Haradinaj was accompanied by his uncle Ljah Brahimaj, who was also indicted and placed in custody at Scheveningen.
Tribunal spokesman Jim Landale confirmed the arrival of the two in the detention unit.
The indictment against them has not been unsealed yet, but they are believed to be accused of crimes against Serbs and Albanian collaborationists. Another member of the Kosovo Liberation Army is also believed to be indicted together with them.
During the 1998/9 conflict in Kosovo, Haradinaj commanded a Kosovo Liberation Army unit in the Decani area, which was considered a stronghold of Albanian guerrillas. His uncle Brahimaj was a member of the unit.
Haradinaj became Kosovo's prime minister after November 2004 elections. At yesterday's government session in Pristina he said he had received the Hague tribunal's indictment and that he was resigning. He also announced he would surrender today.
Seeing him off at Pristina's airport were about 200 supporters. He was transferred to Rotterdam aboard a Kosovo Force plane.
Officials of the UN Mission to Kosovo and the NATO-led Kosovo Force said the situation in the UN-administered province was calm and that no incident had taken place. They added additional security measures had been taken following Haradinaj's resignation.
The government held an extraordinary session today, assessing the situation in the province was calm and that no incidents had occurred. The government offered the UN Mission guarantees for Haradinaj's release pending trial.
The government requested postponing a meeting on missing persons with representatives of Serbia's authorities scheduled for tomorrow.
A parliament session scheduled for tomorrow, which was to consider decentralisation in Kosovo, has been postponed until further notice.
Citizens rallied in protest against the Haradinaj indictment only in Decani, his birthplace. About 5,000 ethnic Albanians protested peacefully.