FORTUNE — Late last month, Apple AAPL notified the Green Electronics Council that it was withdrawing its entire product line — including 39 green-certified desktops, notebooks and monitors — from the organization’s Electronic Product Environmental Assessment Tool program, and that the company would no longer be submitting new products for EPEAT environmental ratings.

“They said their design direction was no longer consistent with the EPEAT requirements,” CEO Robert Frisbee told the
Wall Street Journal
. Frisbee noted that the structure of the new MacBook Pro with Retina Display would have made it ineligible for certification. “If the battery is glued to the case it means you can’t recycle the case and you can’t recycle the battery,” Frisbee said.

EPEAT is one of more than a half-dozen government and industry-supported green computing standards organizations, of which the EPA’s ENERGY STAR program is probably the best known. In its elaborate Apple and the Environment Web presentation, Apple boasts that it’s “the only company in our industry whose entire product line not only meets but exceeds the strict energy guidelines of the ENERGY STAR specification.”

But the withdrawal from EPEAT is a setback to Apple’s campaign to undo the damage to its reputation inflicted by nearly a decade of Greenpeace protests.

And it could have a material effect on Apple’s efforts to sell more of its products into government markets. In 2007, President George W. Bush signed an executive order requiring all federal agencies to use EPEAT when purchasing computers.

According to EPEAT’s registry of participating manufacturers, Dell DELL has 171 EPEAT-certified products, Lenovo has 197, Hewlett Packard HPQ has 221, and Samsung has 309.

Apple, as of last month, has none.