In a statement posted on the National Audit Office's website, Bengtsson cited his poor health and "questioning" of his independence as reasons why he is stepping down.
"The questioning of my independence, combined with my health, allows me to now conclude that I do not have the power, the strength and the commitment necessary for me to fulfill my duties as auditor general," he said in a news release.
The National Audit Office, or Riksrevisionen in Swedish, is a watchdog that oversees how the state's money is used, and how it is accounted for. It is supposed to be politically neutral and independent, but reports this summer by the daily Dagens Nyheter have disputed that. In July, another auditor general resigned after it was revealed she showed internal documents to some of those being audited, and intervened to get friends into positions at the office.
Dagens Nyheter reports that it confronted Bengtsson on Tuesday with information regarding his actions in an unnamed case. The newspaper did not divulge any details from the case but said it would publish "new revelations about Ulf Bengtsson's contacts" later on Wednesday.
Bengtsson, in a letter sent to employees, said new media reports would surface during the coming days. He explained in the letter that he suffered from a "serious illness" during the year and that the reports were "about a conversation I had with the head of an authority during an ongoing investigation. The call was made during my period of illness and my recollection is that it was about my health. But it's one's word against another's."
Bengtsson was appointed auditor general in August 2015. The Swedish Parliament will now consider whether to accept his resignation.