Johnson is contracted until December and the RFU, under previous chief executive John Steele, decided there was no need to engage in contract negotiations until the tournament is over.
After leading England to their first Six Nations title in eight years, Johnson hinted he would like to continue in a job he finds "very addictive".
If Johnson still feels the same after the World Cup, then Thomas would welcome the chance to sit down and discuss the future with him.
"Martin is such an honest assessor of his own performance that he will judge himself after the World Cup," said Thomas, who on Sunday stood down as RFU chairman but will run the day-to-day union affairs until the new year.
"He will turn around and say he is pleased with what he has done and he is staying or that, because he is very self-critical, that he is not happy.
"There is unlikely to be a CEO before January. I will have no problem in sitting down with Martin after the World Cup and resolving his position in the interests of England and the coaching team."
The upheaval in the corridors of power at the RFU should have no affect on England's chances of success at the World Cup, which kicks off against Argentina on September 10.
England's players are on a week's break from their summer training camp.
They will gather back at Pennyhill Park next Monday for the build-up to the August warm-up internationals against Wales, home and away, and Ireland.
"I have spoken to Martin Johnson and the coaches. They said to me that what was going on at Twickenham was not on their radar. The players are not interested in what is happening here," said Thomas.
The RFU will enter the World Cup, at which England will collect the baton as host nation of the 2015 tournament, without a permanent chairman or chief executive in place.
Paul Murphy, the RFU vice-president, will act as interim chairman until a special general meeting is called to elect Thomas' permanent replacement.
The earliest that can happen is October 8, two days before England's World Cup campaign begins. For logistical reasons it is likely to take place some weeks later.
An RFU spokesman insisted there is no pressure to appoint a chairman at the earliest possible juncture "just for presentation purposes".
He confirmed there would be no issue with holding the SGM during the World Cup because only the president, Richard Appleby, and Thomas would be in New Zealand on official duty.
Meanwhile, the process to appoint a new permanent chief executive is beginning to grind into action.
It is understood that Ian Metcalfe, chairman of the Professional Game Board, has agreed to head the interview panel. The other members are yet to be appointed.
The RFU had been decided before yesterday's council meeting that Thomas would play no part in the recruitment, having been on the panel that hired Steele.
The review panel looking into the vexed issue of how a performance director should fit into the RFU's structure, headed by Rob Andrew, are yet to report back with any conclusions.
Steele's flawed attempts at recruiting a performance director - a process which included twice changing the job description - were at the heart of his demise.
Steele had originally envisaged appointing a performance director to oversee the whole England structure, from the senior team to age-group and academy level.
It was a job many felt had Sir Clive Woodward's name written all over it. Nigel Melville, the former England scrum-half, withdrew his application when he realised Woodward was in the running.
But Steele got cold feet and removed the England Test team from the job description - only to be press-ganged into reinstating it by the RFU board.
The RFU still do not know what kind of an appointment they need - someone to oversee the entire England structure, to be Johnson's boss, or someone to concentrate solely on player development.
Andrew, Bill Beaumont, John Spencer, Richard Hill and Jason Leonard were commissioned to investigate how other rugby unions utilise the role.
"Do we need a performance director or something in a different form?" said Thomas.
"We are taking soundings from the IRB and Wales, looking at what others are doing, and we need to get someone in place. We have to get this right. We cannot afford to get it wrong."
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