The 49-year-old quit on Tuesday night after details of her monthly salary were leaked.
The former sports minister was being paid 14,666 euros before tax, nearly as much as the French president or prime minister, who earn 15,140 euros per month, according to Le Monde.
Speaking on France 2 TV, Jouanno said the question being asked about her salary were legitimate. "I've decided to step away from the national debate because it will be difficult to ensure the calm that's needed for the talks," she said.
Prime Minister Edouard Philippe said Wednesday he regretted Jouanno's departure, "However it is important to say that this is just one episode in the story. What counts is the debate and not individuals."
The government said that a new set-up would be announced ahead of Macron's proposed letter to the French people next Tuesday about why the debate was needed.
Rising prices has emerged as one of the chief grievances likely to be discussed during the debate which will gather up comments from scores of suggestions books at town halls throughout the country.
"Something has to come out of these consultations," said Vanick Berbérian, the head of the rural mayors association. "President Macron must give precise terms in his letter so that people feel it will be worth taking part."