The International Criminal Tribunal for the Former Yugoslavia (ICTY) indicted him on war crimes charges and in 2000 he was sentenced to 45 years of prison.

In July 2004, the ICTY, on appeal, determined that his command responsibility for most of the charges was non-existent and his sentence was lessened to nine years imprisonment.

Blaškić was in command of the HVO troops in the Lašva Valley in central Bosnia, which was inhabited, in the majority, by Muslims and Croats.

This peace plan gave definition to a decentralised Bosnia-Herzegovina, organised into ten provinces, each benefiting from substantial autonomy and each being administered by a democratically elected local government.

The decision did not assess the nature of Croat-Muslim war in Bosnia in 1993–94; it accepted the defense claim that there existed a "double chain of command".

It reduced Blaškić's prison sentence to nine years, purportedly due to his good behavior, clear prior record, poor health, voluntary surrender and his young children.