Thomas, who joined the organisation in January 2009 in the newly-created role of corporate communications and public affairs director, is understood to have felt his position had become untenable.
His departure, officially by mutual agreement, comes at the end of a damaging two months at Twickenham.
The RFU are without a permanent chairman, chief executive, finance director or head of human resources and they are no nearer to deciding how a performance director will fit into the management structure.
John Steele was axed as chief executive at the start of June, a decision which prompted Craig Preston to quit just three days into his new job as head of people development.
Martyn Thomas then stood down as RFU chairman - although he remains the acting chief executive - following a damning report into the union's handling of Steele's departure.
Judge Jeff Blackett's review is understood to indicate Peter Thomas had lost the support of some board members, although his conduct was defended in the report.
Disciplinary officer Blackett considered his own position after Martyn Thomas threatened legal action for defamation in the event of the publication of the report, which was thought to call on him and eight of the RFU's nine non-executive board members to stand down immediately.
Blackett remains in the honorary role, despite the non-publication of the report, but has called on the RFU board to address the problems which have left them in such turmoil.
News of Peter Thomas' departure came in a letter from Martyn Thomas to the Rugby Union Writers' Club, which stated: "By mutual agreement Peter Thomas currently corporate communications and public affairs director will be leaving the RFU with immediate effect.
"There are no plans to replace Peter."
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