In August of that year he caused controversy by claiming during a speech that the VFA were engaged in dishonest practices, offering league players inducements to leave their clubs and cross to the association.
The vice-president of the VFL distanced himself from Harper's comments, pointing out that he'd only been involved in football administration for a year and couldn't speak with any authority. The VFA also attacked him for his comments, and the secretary of the association threatened to resign if action wasn't taken in regards to the matter.
He remained secretary until resigning on 5 May 1910 to the pressure of business, ill-health and a family bereavement. Players penned a letter asking him to reconsider his decision but he stayed retired.