The controversial Newsnight episode which led to Lord McAlpine being falsely accused of child abuse was a co-production between the Bureau and the BBC.
Prior to the broadcast of that show, Overton had written on Twitter: "If all goes well we've got a Newsnight out tonight about a very senior political figure who is a paedophile." The tweet has since been deleted.
A statement from the Bureau read: "Iain Overton has resigned his appointment as Editor of The Bureau of Investigative Journalism.
"Deputy Editor, Rachel Oldroyd, will assume responsibilities for editorial control of The Bureau. An appointment of an Interim Editor is likely to be announced in the near term."
It continued: "An inquiry to establish the role of The Bureau in the story is in urgent progress. An interim report will be issued as soon as possible.
"Trustees reaffirm The Bureau's commitment to fact-based, non-sensational investigation in the public interest. Any role by the Bureau or its officers in this story was strictly contrary to the fundamental principles and standards of the Bureau."
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On November 10, Overton launched a defence of the Bureau with a series of posts on Twitter.
"The Bureau of was established to apply the highest standards of investigative and fact-based journalism in the public interest," he said.
"During first 3 years, the Bureau has won major awards for its journalism and built reputation for quality and avoidance of sensationalism.
"The governing Trust of The Bureau does not endorse any material or output that fails to meet these standards."
He added: "The Bureau was named as a contributor to the broadcast of a BBC Newsnight programme on November 2nd on child abuse in North Wales.
"The Trustees are appalled at what appears to be a breach of its standards. To the extent the principles of The Bureau have been ignored by involvement in this story, action will be taken against those responsible.
"The Trustees must ensure that due process is applied and are establishing the key facts. I will make a statement once I have met the Trust."