Thousands of people were persecuted by the HVO while Praljak was the HVO chief-of-staff in 1993, the prosecutor told the Hague-based UN war crimes tribunal.
It is impossible that he did not know about persecutions of such extent, Stringer said.
Praljak freely moved in the entire area under his control and showed that he was acquainted with all that was going on, Stringer said.
He dismissed the defendant's claims that he had not known about thousands of Muslim men being detained in camps set up in the area under the control of Herceg Bosna and that he had had nothing to do with those camps.
According to the prosecutor, Praljak also knew about the conditions in those camps and should have taken steps to improve them.
The prosecutor dismissed a claim by the defence team that men detained in those camps were potential soldiers, as the inmates were civilians.
Apart from Praljak, another five former Bosnian Croat civilian and military leaders are standing trial at the ICTY in this case dubbed Prlic and Others.
They are charged according to personal and command responsibility for crimes against humanity, grave violations of the Geneva Conventions, and breaches of laws and customs of war committed against Bosniaks and other non-Croats in the areas of Bosnia and Herzegovina which they wanted to annex to Croatia.
Their trial started in April 2006. The defendants have been in the Scheveningen detention centre since 5 April 2004.
The presentation of closing arguments started on Monday.