The Lancashire opener will fly home from Pakistan, where England are preparing for a one-day tournament in Sharjah. He will consult further expert opinion and undergo treatment, a process that could sideline him for several months.
"To be honest, declaring myself unfit is a weight off my mind," Atherton said last night, speaking from his hotel in Lahore. "I'm disappointed because I really worked hard in Cape Town, where I've been playing with Lancashire, and I felt I'd achieved full mobility.
"But two long air flights, which have made my back stiffen up again, have shown me that it's not properly right. In light of that, and the fact that I've had enough of trying to play when not 100 per cent fit, I had no choice but to pull out. I now want to have a period of rehab to get my body properly right, which I am confident I can do."
Lengthy air journeys - his two trips took the best part of 35 hours - were not the only factors at play. Atherton felt that the need to prove his fitness, although understandable from the selectors' point of view, was rushed.
"After the denervation I had a month ago [a procedure whereby the nerve sending pain from his back is killed off] I felt a more gradual build- up, rather than the mad two days of running around at Lilleshall that I did, would have been better. I have no gripe, though - the selectors and the captain needed to know."
Atherton was one of four World Cup players specifically required to prove their fitness in Lahore and Sharjah and the selectors will have already earmarked potential replacements for the former captain, whose selection was largely down to his skill as a technician on green pitches.
Presuming England will replace like with like, then the role will probably fall to Nasser Hussain or Mark Ramprakash, though the Leicestershire pair of Darren Maddy and Ben Smith will also be considered. Either way, the selectors must decide by today, the deadline by which 15-man World Cup squads must be named.
Selecting Atherton for duty has become something of an act of faith over recent months, with neither player nor physio able to guarantee fitness for more than a few hours. In fact, over the last eight months his back has forced him to pull out of Tests three times, sometimes on the morning of the match. Such uncertainty can affect both tactics and morale, particularly within the confines of a 15-man squad, where replacements are strictly vetted.
Given the nature of his problems - a chronic inflammation of the vertebrae has recently been exacerbated by a disc problem - it is something of a minor miracle he has played so often. Before his withdrawal from the Test against Sri Lanka last August, he had managed 62 Tests appearances on the trot, most of them as captain.
This time he did not even make it to the nets in Lahore, where England are acclimatising for the Coca-Cola Cup in Sharjah.
"Michael let me know soon after he woke up," revealed the chairman of selectors, David Graveney, who is also managing England's trip to Lahore and Sharjah.
"Michael knew he was back to square one," admitted Graveney, "so he didn't try to hide or conceal it. We appreciate his honesty, but we're very disappointed for him because we know what he's been trying to do over the past two months to get fit. He could perhaps have tried to get through the next few weeks, but by making a bold decision now, he's again shown that he's a team man."
Graveney was less forgiving over what Atherton, now 31 and with a possible four to five years more Test cricket in him, would have to do to gain selection in future. "We as selectors need him to prove to us over a lengthy period of time that he is injury-free, and that would mean playing on a regular basis for Lancashire," he said.
Atherton's iron will may just ensure that the recuperation period, however long, is not a futile one.