Czech Klimkova, who coached the Football Ferns to their first World Cup match win last year on home soil, departs with immediate effect after managing only 11 victories from 39 games.
Klimkova went on leave in May after the New Zealand Football (NZF) launched the investigation and was then cleared in June.
She was to resume her role for the Paris Olympics but in an NZF statement in early July she said it was not the right time to return citing the team environment and an incomplete "restorative process".
Under interim coach Michael Mayne, New Zealand crashed out of the Olympic group stage with three straight defeats while shipping six goals.
Mayne will nonetheless remain in the role while "campaign planning" continues for the 2027 World Cup, NZF said.
It added that Klimkova will work for NZF for the next six months supporting the high-performance department and national team activity.
"I want to thank Jitka for her time as Ford Football Ferns head coach and the major role she has played in bringing through a new generation of players," NZF boss Andrew Pragnell said in a statement on Friday.
"She will forever be remembered as the coach who led us to our first ever FIFA Women's World Cup win, a historic, game-changing moment for football in Aotearoa New Zealand."
Though not short of resources or match practice before the World Cup, the Ferns slumped to a record low in the world rankings under Klimkova and now languish at number 31.
"This experience was a challenge and made me stronger," Klimkova said in the NZF statement.
"I believe now is the right time to step away and let another coach carry on."
