Jamshid Sharmahd was arrested in complicated operations launched by the country’s security forces, the ministry said in statement, IRNA reported.
The Intelligence Ministry added that its forces have dealt a “heavy and serious blow” to the terrorist group, according to the statement.
The ministry said it will give more details of the arrest later.
Sharmahd, who was leading armed and sabotage operations inside Iran, is now in the powerful hands of Iran's security forces, the statement said.
The statement did not elaborate on where or when the leader of the group known as the Kingdom Assembly of Iran, or Tondar (Farsi for thunder), was arrested.
According to the statement, he had orchestrated the April 12, 2008 bombing in a Husseynieh in Shiraz that killed 14 people and wounded 215.
Iran hanged three men convicted of the bombing in 2009, saying they had ties to the terrorist group.
It said they had been taking orders from an Iranian US-backed "CIA agent" to try to assassinate a high-ranking official in Iran.
Iran hanged two other convicted members of the group in 2010, who had "confessed to obtaining explosives and planning to assassinate officials".
The statement issued on Saturday said that Tondar had plotted several other "big operations" which failed.
It said that Tondar had planned to blow up a dam in Shiraz, use "cyanide bombs" at a Tehran book fair, and plant an explosive device at the mausoleum of the founder of Islamic Republic, Imam Khomeini.
AFP contributed to this story.