The Hawza, or Marjaiya, is based in Najaf and represents the highest spiritual authorities for Shia Muslims in Iraq and Iran.
Made up of five senior clerics, it has previously given support to the United Iraqi Alliance (UIA) which won the 2005 elections and became Iraq’s ruling coalition.
But al-Sistani renewed his call for Shia clerics to remain neutral in this year's vote after one of his top Hawza associates launched an attack on close allies of Nuri al-Maliki, the Iraqi prime minister.
"There are people in the executive authority who have betrayed the country, who have stolen public money or create sectarianism in the country like Education Minister Khudair al-Khuzai."
Al-Maliki has defected from the ruling Shia coalition with several allies to form a rival party.
Reacting to the defection, Ayatollah Bashir al-Najafi unleashed a withering attack on key allies of al-Maliki, accusing them of negligence and corruption.
"There are people in the executive authority who have betrayed the country, who have stolen public money or create sectarianism in the country like education minister Khudair al-Khuzai", al-Najafi said.
The cleric also slammed "corruption and negligence in most fields providing services to the population like water, electricity, agriculture, oil and ration cards."
Al-Najafi also named and criticised the acting commerce minister, Safaldin al-Safi, who is responsible for the ration card system, and Hussein al-Shahristani, the oil minister.
Both are standing for election as part of al-Maliki's State of Law bloc, as are Karim Wahid, the minister for electricity, and Ali al-Bahadli, the agricultural minister.
Nevertheless, al-Sistani argues that the Hawza should restrict itself to spiritual guidance and not adopt a political role like that championed in Iran by the late Ayatollah Ruhollah Khomeini or the current Iranian supreme leader, Ayatollah Ali Khamenei.