The Warriors, who were relegated from the English Premiership in September after going into administration, did not apply to play in the Championship as they will merge with fourth-tier side Stourbridge and change their name to "Sixways Rugby".
"We realise that the disappointment felt by Worcester Warriors staff, players and fans following the Atlas decision will be very significant," RFU Chief Executive Bill Sweeney said.
The merger with semi-professional Stourbridge is subject to a vote of the lower league club's members, and would require RFU approval, but if it goes ahead it could mean Worcester's new owners would avoid having to pay millions of pounds owed to creditors, including former players and staff.
However, the decision to withdraw the Championship bid leaves the RFU with no statutory means of enforcing payment from rugby's creditors as the governing body's priority had been to enable the club to play in the Championship as well as Worcester Warriors Women in the Premier 15s.
"For a club to continue after insolvency, it is imperative that it has a sustainable and funded business plan, that there is transparency about ownership and funding structures, and that rugby creditors are paid," Sweeney added.
"We will continue to work with Atlas over the coming weeks to understand their vision for rugby at Sixways."
The RFU has reached an agreement with Wasps, who also went into administration last year and were relegated from the Premiership, to prioritise the payment of staff and players as the club meet RFU requirements and they will have a place in next season's Championship.
