Now guide author Hayden Shearman has apologised to anyone who took offence at the suggestions.
He has since revised the controversial paragraphs removing references to whistles and loose-fitting clothing.
The latest suggestions include running in daylight or well-lit areas, alternating running routes randomly, running with company or in populated areas, letting others know the planned route and return time and dressing appropriately for the exercise and the environment.
Shearman said he never intended to support the idea that women were to blame for gratuitous attacks.
The suggestion was written weeks after a female friend was attacked at knifepoint while running.
"I wrote this section in consultation with her, somewhat in the heat of the moment. No one should ever go through an horrific attack like this and I hoped this book would encourage more women to feel safe while running. As you can imagine, this incident shook me, and the victim, and has since influenced where I live and where, when and how I run."
He said criticism directed towards the Shoe Clinic was misdirected and unwarranted.
The second edition of the runner's guide was produced with support from the running chain, which was in no way responsible for the book's contents.
Shearman, who manages a running coaching business, said he was focused on getting people moving to stay healthy and encouraged people to look out for each other and take back our streets.
Wellington Women's Refuge manager Philippa McAtee said women shouldn't have to protect themselves from being attacked.
"Men shouldn't be attacking women," she said.
"I guess he meant well but women shouldn't have to have strictures on them like to wear loose clothing to protect themselves from attack."
Duck Patten, who organises a female-only running group in Wellington called JogSquad said the comments were "ridiculous" but could understand why Shearman had written what he did.
"For me I've never had a problem with running Wellington tracks or in the city or anything like that," she said.
She was skeptical over the wolf whistle comments as well.
"Taking it as a compliment . . . hmm, ah, I don't think so.
"It's a funny one because, like, when we're out running, slogging our asses off, the last thing you want is a wolf whistle."
Encouragment from passers-by was welcome though, she said.
"My overall impression is it's pretty crap advice, really, I would say. As a runner, I wouldn't be that happy about reading that."
Patten said she understood why Shearman had written the advice in response to his friend being attacked.
"That would be a horrific thing to go through, but far out, we shouldn't have to wear certain things to feel safe.
"I really hope that New Zealand stays a safe enough place that we can always go out and do whatever we wants wherever we want."
LISTEN: Wolf whistling still a common harassment faced by women..
