Suradharma Ali says his alleged involvement in the multi-million dollar case is all a misunderstanding and the matter should be cleared up soon.
The Corruption Eradication Commission spokesman John Budi says there was "alleged corruption in the hajj pilgrimage process between 2012 and 2013" and Ali had been named a suspect.
The commission, known locally as the KPK launched an investigation after suspicious transactions worth $US20 million were detected in the fund.
Mr Budi said the loss to the state was still being calculated but the government had paid out more than $US86 million in those years to fund the hajj.
Indonesia, which is home to more Muslims than any other country, sends a huge number of people on the annual pilgrimage to the holy city of Mecca in Saudi Arabia.
Yearly pilgrim quotas mean they wait years and pay thousands of dollars to reach Mecca.
The Ministry of Religious Affairs oversees a kind of trust fund that holds people's deposits.
Mr Ali, who has refused initial calls to step down, is the latest high-level figure from President Susilo Bambang Yudhoyono's outgoing government to be mired in a corruption case.
Indonesia is ranked 114th out of 177 countries and territories in Transparency International's Corruption Perceptions Index.