Endometriosis occurs when tissue similar to the womb lining grows in other places, usually within the pelvic cavity.
"I know you'll respect that my health comes first and at this time I've got to prioritise what I need to do for me," Hayes said in a statement on Thursday, addressing the fans.
"Throughout my absence, Denise Reddy will be making the on-field decisions along with Paul Green who will be carrying out all press obligations on my behalf.
"We have built a tremendous team over many years and we've adopted a very multi-disciplinary approach so that if situations like this arise, we are capable of being able to respond to the challenge. We have full confidence in Paul, Denise and all of the staff."
She led Chelsea to five titles in the Women's Super League, said she is now in recovery and that Denise Reddy and Paul Green would take charge of the team in her absence.