Thomas has stepped down as RFU chairman following a six-year tenure.
But he will remain in three other key roles at Twickenham - acting chief executive, chairman of Rugby World Cup 2015, which will be staged in England, and as an RFU representative on the International Rugby Board.
Sunday's developments followed a four-hour RFU Council meeting to discuss findings of the Blackett Review panel, which looked at circumstances surrounding the hiring and firing of former Twickenham chief executive John Steele.
The report put together by the five-man group, headed by RFU disciplinary officer Judge Jeff Blackett, will not be made public. Sections of it are thought to be highly critical.
Decisions reached by the council included Thomas withdrawing his nomination for board chairman at the RFU AGM that took place this afternoon; council member Paul Murphy being appointed interim chairman; and the whole RFU board being given a vote of confidence.
But less than nine weeks before the 2011 World Cup kicks off in New Zealand, the RFU has no permanent chairman, no permanent chief executive and they are still searching for their first performance director.
The performance director job, a role created by Steele's review of the organisation earlier this year, had been thought to be tailor-made for England's 2003 World Cup-winning mastermind Sir Clive Woodward.
But during the course of a bungled RFU process, Woodward reaffirmed total commitment to his current employers, the British Olympic Association.
"Most people would not be comfortable with being chairman and acting CEO. The staff made it clear to me last week they wanted the stability of the last month maintained," said Thomas.
"I discussed with the board last week whether you could do both jobs. I left the meeting and they discussed it for 90 minutes, looking at all manner of options.
"I was never comfortable with doing the two jobs. The board felt it would be better if I stayed as acting CEO, having done the job since John left.
"If I had not been acting CEO, I would not have felt the need to stand down as chairman (because of the report).
"I said that if the council did not have the confidence in me to do the job I would walk away. You have to have the confidence of the people around you.
"What was important was what the staff told me last week. They did not want another change. They wanted stability. English rugby is in a healthy shape - it is not a message of doom and gloom."
The review panel, which also comprised RFU council members Geraint Ashton Jones and Malcolm Wharton, intended investigating everything from Steele's recruitment to the board's loss of confidence in his leadership and the process leading to the termination of his contract.
The botched recruitment process for the performance director position, which played such a key part in Steele's downfall, was also due for scrutiny, in addition to the board's governance.
The management board ousted Steele from his post at an emergency meeting last month after deciding his position had become untenable.
Thomas added: "No-one can be happy or proud at what happened when a senior person left in the circumstances he did. The board and I have to look at that and consider the recommendations we need to make.
"The report (Blackett Review) is the view of five individuals, and I have not had the chance to respond to it.
"The criticisms are fine. Some I have no problem with; others there need to be a discussion about. I would want to put my point of view to the panel at some stage.
"I regret the situation that occurred with John. Could we have handled the process better? Probably. It is easy to point a finger and say this could have been done better. Overall, what we delivered was right, but you can always do better."
Blackett, meanwhile, said: "The panel worked tirelessly over the last three weeks to gather a huge amount of evidence, and we felt our recommendations were valid and appropriate based on that evidence.
"As guardians of the game, though, council had some important decisions to take and discussions were robust and emotive in that regard.
"I would like to thank my panel for a job well done and hope that as a game we can now draw a line under the events of the past few months and get on with rugby."
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