The Iranian official's remarks came after a terrorist attack on Shiite Pakistanis last week that left at least 45 dead in Karachi.
"The most ruthless incidents and bombings are carried out against the Shiites in Husseiniyas and mourning ceremonies and people are martyred," Pourmohammadi said, addressing a ceremony in Tehran on Saturday.
He urged Islamabad to take swift action to put an end to these heinous crimes.
Last week, the Iranian Foreign Ministry strongly deplored the killing of Shiites in Karachi and urged the international community to launch a serious campaign against terrorism.
In a statement, the ministry expressed sympathy with the relatives of the victims, and added that such terrorist moves serve the divisive policies of the enemies of Pakistan's Muslim nation and harm the country's interests.
The statement called on the Pakistani government and prominent religious figures in the country to take proper actions to prevent similar attacks in future.
The statement also asked the international community to play a serious role in an all-out fight against terrorism which is considered as a threat to all nations.
Police officials announced later on Sunday that at least 45 people have been killed by the bomb explosion in Karachi.
The blast in the mainly Shiite Muslim area of Abbas Town destroyed several buildings and set others on fire. Some reports spoke of a second explosion.
No group has yet said it planted the bomb, which went off near a mosque as worshippers left evening prayers.
