Daniher told the Eagles hierarchy of his intentions to scale back his role at a staff meeting on Thursday morning.
List manager Craig Vosso will be promoted to general manager of football operations.
The announcement continues the upheaval of the Eagles football department following the resignations of senior coach John Worsfold and assistant coaches David Teague and Phillip Walsh.
"Unfortunately, I do need to focus a lot of energy on my own health and wellbeing at this stage and the role of football operations general manager is quite demanding," Daniher told the Eagles website.
"I don’t believe I could commit the time needed to be effective, so it is important to recognise that and bring someone in who can contribute as required.
"I will assist Craig during the transition period and will remain with the club, doing what I can to ensure we improve quickly.
"I would also like to thank the club for the great support they have offered me and we all look forward to 2014 with optimism."
The move comes at a difficult time for the Eagles as they are less than a week into the search for a new senior coach.
Chief executive Trevor Nisbett, who is part of the sub-committee charged with finding the new coach, told the Eagles website that the club was supportive of Daniher's situation.
"I have been aware of – and talking to Neale – about his personal position for the last few months," Nisbett said.
"Neale has made an outstanding contribution to the football club in the very demanding role of general manager of football operations, but he needs to focus on his own health.
"He has been leading the way with the review of the football department for the last month or so and has provided some strong direction for the future.
"While he needs to peel back his own work commitments, he will remain in an administrative role at the club and will support Craig’s transition into the role.
"It will mean a re-structure within the football department and in that respect we are fortunate to have someone of Craig’s ability to step into the position."
