To address governance issues arising from Thomas' dual role, Peter Baines, as senior non-executive, replaces him as chairman.
Thomas and Baines begin their new duties immediately and will revert to their previous positions on the day the new CEO takes up office.
The review group established to examine the performance director role that many think is ideally suited to Sir Clive Woodward has yet to meet so no discussions on the position have taken place.
The process to appoint a new CEO is expected to take between six to nine months and a small panel has been formed to lead the search.
The panel, whose chairman will be appointed in the next 48 hours, has been given the authority to select headhunters if required.
The RFU were heavily criticised for their role in the botched appointment of Woodward as performance director by John Steele, whose brief and ill-fated reign as CEO ended earlier this month.
"The board felt it was important, at the current time, to maintain stability in the union in challenging times," said Baines.
"Martyn has done an excellent job in taking over the day-to-day running of the union since John Steele's departure.
"It was felt he was the best person to continue until a new CEO is chosen.
"In addition we have taken important decisions around other key issues of governance and around securing the futures of key staff. It was a positive and productive meeting."
Francis Baron, Steele's predecessor at Twickenham, recently claimed that the governing body is on the brink of "complete meltdown".
Thomas, however, believes the union is in rude health.
"It's important to remember that the RFU itself is in a good position despite recent events," said Thomas.
"We are set to end the year by beating our budget targets and performances on the field this season by our senior team, Saxons, U20s and Women's team have all been strong.
"Finally we have just announced our new Choose Rugby initiative to drive recruitment and retention in our clubs with the O2 Touch programme as the first element of that.
"So while we accept recent weeks have been challenging there are many good things happening and I am greatly excited by the privilege of leading the RFU as acting CEO."
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