In a resignation letter sent to Prime Minister Justin Trudeau, Johnston articulated the role has become too cluttered in political controversy for him to continue.
"When I undertook the task of the independent special rapporteur on foreign interference, my objective was to help build trust in our democratic institutions," he wrote.
"I have concluded that, given the highly partisan atmosphere around my appointment and work, my leadership has had the opposite effect."
The former governor general has continued to dispute claims of bias owing to his personal relationship with the prime minister. He condemned the "baseless accusations" against him that "diminish trust in our public institutions."
"I have been fortunate in my public life to have served as chair of or member of advisory committees or task forces on dozens of occasions over the years, with appointments by prime ministers, several premiers, several ministers and on none of those predication has my impartiality or integrity has ever been questioned," said Johnston.
On May 23, Trudeau's 'special rapporteur' unveiled his initial report on foreign interference, stating a public inquiry into Chinese election interference is 'unnecessary,' but added he would conduct public hearings into materials that are not "classified."
"When I began this process, I thought I would come to the same conclusion that I would recommend a public inquiry," said Johnston, acknowledging that opposition parties have repeatedly called for an independent, public inquiry.
The 'special rapporteur' said a public review of classified intelligence "cannot be done," but he recommended Trudeau invite national security agencies to review the conclusions of the Inquiry report.
He also requested the three Opposition leaders be invited to those deliberations as part of a "necessary step in transparency and accountability."
According to the resignation letter, Johnston will step down after delivering a brief final report.