He voiced confidence that he would prove his innocence and that the prosecution did not have evidence against him.
He also said he expected a swift trial.
Australian Judge Kevin Parker pledged he would do everything so the trial could start as soon as possible, but reminded Boskoski that there were many cases awaiting trial.
The 44-year-old Boskoski, who was Macedonia's interior minister from May 2001 to November 2002, has been charged with three counts of murder, cruel treatment and wanton destruction of villages as violations of the laws and customs of war committed by Macedonian police in a 12 August 2001 attack on Ljuboten, a village near the capital of Skopje, during a clash with ethnic Albanian rebels.
The outcome were seven dead Albanians, while 100 were imprisoned and mistreated. Some 30 houses and barns were set on fire or demolished.
Boskoski, who has dual Macedonian-Croatian citizenship, was transferred to The Hague on March 24. Since 31 August 2004 he had been detained in the northern Croatian seaport of Pula based on an arrest warrant issued by Skopje, where he was charged with the death of seven Asian immigrants whom Macedonian police killed on the state border in 2002.
When the Hague tribunal's indictment was read to him at Pula's County Court, Boskoski said he was not guilty but added he would surrender because he recognised the legitimacy of the UN Court.
He has been indicted alongside Johan Tarculovski, a police officer who led the Ljuboten attack and who has been in detention in The Hague since March 17.
Boskoski will be represented by Zagreb attorney Anto Nobilo.