Dr Richard Freeman has resigned from his role with British Cycling due to ill health.
Freeman, who has been off work with a stress-related illness, was at the centre of an investigation regarding the contents of a medical package delivered to Sir Bradley Wiggins at the 2011 Criterium du Dauphine.
British Cycling chief executive Julie Harrington told the Guardian: "We were investigating him on employment matters and UKAD (UK Anti-Doping) were investigating him on doping matters.
"After some months we were ready to continue with disciplinary action. Dr Freeman really wasn't well enough to commence that and so we've allowed him to resign.
"We continue to support UKAD and when Dr Freeman is better I would hope he would continue to support UKAD with any ongoing investigation.
"It is an area that for the sake of our current riders, membership and the reputation of our sport, that I would have hoped to have brought to a tidier end, but we also have a duty of care to him as an employee."
Freeman was heavily criticised by MPs during March's Culture, Media and Sport select committee hearing into the allegations surrounding the GB squad and Team Sky for failing to keep adequate records of the treatment he gave riders, most notably 2012 Tour de France winner Wiggins.
He gave a written statement to a parliamentary hearing in which he insisted the Jiffy bag sent to Wiggins contained the legal decongestant Fluimucil, rather than the the banned corticosteroid triamcinolone.
UKAD was unable to verify the contents because Freeman's medical records were missing.
Harrington continued: "You've also got to have the right processes and systems in place to ensure there's no oversight, and an evidence trail so if something goes wrong you can find out where it's failing.
"You've got to have the ability to defend your clean riders."
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