Former Yugoslav deputy premier Nikola Sainovic is the second member of Milosevic's inner circle to surrender to the court in a week.
He is charged along with the ousted Yugoslav president over alleged mass killings and expulsions of ethnic Albanians in 1999.
Sainovic, dressed in suit and tie, pleaded not guilty to each of five counts of violations of the laws and customs of war and crimes against humanity as they were read out to him by a court official in the Netherlands.
His surrender is a landmark for tribunal prosecutors after they indicted Milosevic and four members of his inner circle for war crimes in Kosovo in 1999. Two have turned themselves in, one has committed suicide and one remains at large.
Sainovic's appearance in The Hague comes hot on the heels of a move by the Yugoslav parliament to pass a law on co-operation with the war crimes tribunal to ease intense financial and political pressure from the West.
Milosevic and his former colleagues are charged with crimes against humanity and violations of the laws and customs of war, including responsibility for the murder of around 900 Kosovo Albanians and the expulsion of around 800,000 from the province.
Milosevic, who has been on trial since February, is accused of genocide and crimes against humanity in Croatia, Bosnia and Kosovo in the 1990s.