The three leaders had been summoned to appear at a Dhaka court on Tuesday but ignored the order, which lead to an arrest warrant being issued, he said.
Haque said the charges stemmed from claims that Nizami's alleged persecution at the hands of the ruling Awami League was akin to the suffering of the Prophet Mohammed, he said.
Jamaat-e-Islami supporters have condemned the arrests as politically motivated because of the group's political alliance with the opposition Nationalist party, led by Begum Khaleda Zia, the former Bangladeshi prime minister.
Many Bangladeshis accuse Jamaat of collaborating with the Pakistani army during Bangladesh's independence war in 1971.
The party in turn has accused the government of Sheikh Hasina of trying to curb its activities using war crime charges and is likely to see the arrests as part of that effort.