Mr Seselj had denied the charges. In his first reaction, he said the court had reached the only verdict possible.
But Croatia`s prime minister condemned the verdict as "shameful".
The UN tribunal`s prosecutor Serge Brammertz said his office would decide later whether to appeal.
"I`m absolutely convinced that the victims` communities and many people will not be satisfied with this outcome," Mr Brammertz said.
Mr Seselj was allowed to go to Belgrade in 2014 after being diagnosed with cancer and was not present in the courtroom.
He had even refused the tribunal`s offer to follow the verdict by video link
He has been taking part in anti-government rallies ahead of Serbian parliamentary elections later this month.
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