The leader of the biggest party in the Serbian parliament faces charges of persecution, extermination, murder and torture of Croats, Muslims and other non-Serbs.
He is accused of organising crimes with the former Yugoslav president, Slobodan Milosevic, who died in March while still on trial - also at the International Criminal Tribunal for the former Yugoslavia (ICTY).
According to the prosecution, his hate-mongering speeches led thousands of Serbian volunteers to sign up and fight in wars in Croatia and Bosnia.
Alphons Orie, the presiding judge, said the defendant's weakened state as a result of refusing both food and medicine did not justify delaying the start of his trial.
He said: "He persists in not taking food ... he persists in being absent.
"The court finds that the accused's self-representation has essentially obstructed the proper and expeditious proceedings."
He instructed standby defence lawyers to take over.
The 52-year-old began his hunger strike more than two weeks ago, demanding free choice of legal counsel, the unconditional right to defend himself and unrestricted visits by his wife.
Seselj was banned from representing himself in August after disrupting pre-trial hearings, but the tribunal's appeals chamber later restored his right to self-defence while assigning a standby counsel should Seselj obstruct proceedings again.
He has accused the ICTY of trying to infect him with a deadly disease and of carrying out "satanic rituals".
Seselj's supporters say he has already had to wait too long for his trial and accuse the UN court - which was set up in 1993 to try crimes committed during the 1990s Balkan wars - of bias against Serbs.
Orie said the prosecution would present 102 witnesses and allotted 81.5 hours of court time to hear them, meaning the prosecution case is likely to last until next spring.