No group immediately claimed responsibility for the attack on Kadhimi's residence in Baghdad's fortified Green Zone.
Iraqi Prime Minister Mustafa al-Kadhimi tweeted the news, identifying the man as Sami Jasim, who oversees the Islamic State group's financial operations and served as the deputy leader of IS under the late Abu Bakr al-Baghdadi.
The probe team had found that Subahani had planned to spread IS activities in Kerala and Tamil Nadu and to assassinate prominent people. Subahani was arrested by the NIA on October 5, 2016.
The Peruvian diplomat served as United Nations Secretary General from 1981 to 1991.
The protests are an unprecedented leaderless challenge to Iraq's Shi'ite Muslim-dominated and largely Iran-backed ruling elite, which emerged after a US-led invasion toppled Sunni dictator Saddam Hussein in 2003.
The US has blamed Iran-backed paramilitary groups for a spate of similar attacks in recent months on the Green Zone, but there has never been a claim of responsibility.
A majority of US airmen stationed at the Al-Balad airbase north of Baghdad had already left following tensions between the US and Iran over the last two weeks.
Seeking to tighten pressure on its foe, the United States meanwhile imposed more sanctions on Iran, responding to an attack on US troops in Iraq launched by Tehran in retaliation for the death of General Qassem Soleimani.
The aviation authority said it will continue to closely monitor events in the Middle East and that it is coordinating with its national security partners.
Iran's Revolutionary Guards confirmed that they fired the rockets in retaliation for last week's killing of Qassem Soleimani.