Iran has been gripped by the scandal ever since the payslips of executives at several public companies were leaked two months ago, showing salaries more than 100 times that of their average workers.
It has provided ammunition for hardline opponents of moderate President Hassan Rouhani less than a year before he faces re-election.
Seyed Safdar Hosseini, a former reformist minister who was hand picked by Rouhani to head the development fund, had been particularly targeted by Iran's conservative media.
His leaked payslip showed he was paid 580 million rials ($17,000) per month.
Hosseini resigned along with the rest of the development fund's management, which oversees investment in infrastucture. Media reports said he had agreed to repay some $140,000 to the state.
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Hosseini was labour and economy minister under reformist president Mohammad Khatami, who was in power from 1997 to 2005, and his daughter was elected to parliament in this year's legislative elections.
The news came just two days after Economy Minister Ali Tayebnia sacked the directors of four banks "for receiving unconventional salaries and loans".
The conservative media have also accused Hossein Fereydoun, the president's brother and special advisor, of influencing the appointment of the head of Refah bank, who was among those fired on Thursday after it emerged he earned some $60,000 a month.
Fereydoun has denied playing any role in the appointment.
Supreme leader Ayatollah Ali Khamenei renewed calls on Saturday for the government to crack down on exorbitant salaries.
The economy minister has set a salary cap of $5,500 a month for bank directors, local media reported, with wider regulations for public companies to follow.
One reformist official, Abdollah Nasseri, claimed hardline opponents of the government have 3,000 payslips of top officials that they intend to use to discredit Rouhani ahead of the election in May.