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Butcher has two more matches in which to rediscover his form ahead of England's first Test against South Africa in Johannesburg.
England had planned to partner the Surrey left-hander with opener Atherton, a right-hander, in a bid to disrupt the South Africans' fearsome pace attack.
But he has scored just 24 runs in his four innings since the start of the tour.
More worryingly, he has not scored a half-century in his last 15 Test innings.
He fell for a duck and was then run-out for just three runs in the most recent match against the Combined Western Province/Boland XI at Newlands.
Although the fault for his run-out fell mainly at the door of Atherton, it will have further dented his draining self-belief.
England captain Nasser Hussain is doing all he can to boost Butcher's confidence, but has made it clear he must make runs in the next two friendlies or face the axe for the first Test.
"At the moment our game-plan is Atherton and Butcher, but Mark's going to have to get some runs and we'll review it every game," said Hussain.
"You have to believe in people and I'm a firm believer in Mark Butcher when he gets into the Test arena. He has the right guts about him to get some runs."
Butcher is keenly aware that the chief candidate to replace him, Yorkshire's Michael Vaughan, is in top form.
He will keep his place for Friday's game against Combined Free State/Griqualand XI at Bloemfontein.
But if he fails against an opposition who have only one player with international experience - England will have to rethink their Test strategy.
Hussain will then have just the four-day game against Northerns/Guateng XI at Centurion to try other options before the First Test in Johannesburg on November 25.
The skipper has further problems in that he is still sweating on the fitness of three key players.
Darren Gough is struggling to be fit even for the game in Centurion never mind Bloemfontein, while fellow bowlers Dean Headley and Andrew Flintoff also need more time to recover.
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