The guide tells women it's a "reality" that even in Wellington they need to take extra care when running, Fairfax reported.
"Find a running club or regular running buddies ... wear loose fitting clothing, run in the day in well-populated areas and interpret whistles as compliments (all the running is obviously paying off)."
Harcourt wrote the comments spoiled an otherwise useful guide book.
She felt that shrugging off wolf whistling downplayed the way they made women feel.
"I think I'll take whistles as what they are: creepy and lame," she tweeted.
"Also it's really not your place to tell female runners to take 'whistles as compliments'."
Other twitter users have also waded in to the debate, questioning advice given to women in the guide.
"Really not necessarily to start the victim blaming in a running guide. Lame," wrote one twitter user.
Shoe Clinic has admitted that part of the guide were poorly worded and undertaken to remove the publication from the store.
"It wasn't our intention to offend anyone," a company employee told Fairfax.
He said the company had sponsored the guide, not written it, and given the guide away to help runners find routes around the city and promote safety.