The iPhone maker asked the organisation to drop all 29 of its hardware devices from the list due to design changes preventing them from meeting its criteria.
EPEAT's standards require environmentally friendly devices to be easily disassembled for recycling purposes, but Apple products do not meet this condition.
"They said their design direction was no longer consistent with the EPEAT requirements," Robert Frisbee, CEO of EPEAT, told The Wall Street Journal.
"They were important supporters and we are disappointed that they don't want their products measured by this standard any more."
Apple previously underlined its commitment to environmental issues, announcing that its massive data centre in North Carolina will be powered entirely by renewable energy sources by the end of 2012.
The company is yet to publicly comment on its decision to remove its products from EPEAT's list.