Benon Sevan announced his decision on Sunday in a scathing letter that lambasted UN Secretary-General Kofi Annan, the Security Council, United Nations critics, and the Independent Inquiry Committee investigating the allegations of corruption against him.
"As I predicted, a high-profile investigative body invested with absolute power would feel compelled to target someone and that someone turned out to be me," Sevan wrote in the letter.
"The charges are false, and you, who have known me for all these years, should know that they are false."
The resignation is largely symbolic because the UN was paying Sevan just one dollar a year to keep him on payroll so he would cooperate with the committee. But it removes his diplomatic immunity and could leave him open to prosecution.
Sevan, a Cypriot citizen believed to be in Nicosia, is also being investigated by the Manhattan district attorney's office.
Former US Fed chairman Paul
Volcker headed the inquiry
On Thursday, Sevan's lawyer Eric Lewis said the committee would find in its upcoming report that Sevan got kickbacks for steering contracts under oil-for-food to a small trading company called African Middle East Petroleum.
Lewis said it would also accuse Sevan of failing to cooperate with the investigation.
The amount of money Sevan allegedly took was not immediately known - and may be as little as $160,000.
In a February report, the committee, led by former US Federal Reserve chairman Paul Volcker, concluded that Sevan solicited oil allocations on behalf of the company, known as AMEP, between 1998 and 2001. It accused Sevan of a "grave conflict of interest".
That report questioned $160,000 in cash which Sevan said he received from his aunt in his native Cyprus between 1999 and 2003.
The report called the money "unexplained wealth" and noted that the aunt, who has passed away, was a retired government photographer living on a modest pension.
The oil-for-food programme, launched in December 1996 to help ordinary Iraqis cope with UN sanctions imposed after Saddam Hussein's 1990 invasion of Kuwait, quickly became a lifeline for 90% of the country's population of 26 million.
Oil sales proceeds were supposed
to be used for ordinary Iraqis
Under the programme, Saddam's government could sell oil, provided the proceeds went to buy humanitarian goods or pay war reparations.
Saddam's government decided on the goods it wanted, who should provide them and who could buy Iraqi oil. But the Security Council committee overseeing sanctions monitored the contracts.
Saddam allegedly sought to curry favour by giving former government officials, activists, journalists and UN officials vouchers for Iraqi oil that could then be resold at a profit.
In his letter, Sevan lashed out at Annan and said the oil-for-food programme was far better run than the Development Fund for Iraq (DFI), the US, British, and later Iraqi-run operation which replaced it after the fall of Saddam in 2003.
Auditors have said billions of dollars in DFI money were mismanaged and contracts were awarded without competitive bidding.
"The charges are false, and you, who have known me for all these years, should know that they are false"
former oil-for-food chief
"The real oil-for-food 'scandal' is in the distortion and misrepresentation of the accomplishments and the record of the programme by now well-established UN bashers," Sevan said.
US critics, particularly Republicans in the US Congress, have frequently cited oil-for-food as emblematic of perceived UN bungling and outright corruption. Some have called for Annan to resign.
The United Nations has fired one staff member over findings made by Volcker's team. Joseph Stephanides was dismissed over accusations that he illegally altered the competitive bidding process for a company to inspect humanitarian goods.