The amalgamation comes after more then a year of He Whānau Manaaki supporting Whanganui's management team and teachers.
"Our work with HWM has demonstrated the beliefs that come with being part of a larger organisation and having access to stable infrastructure and a wide range of professional and operational expertise and resources," WKA general manager Trish Taylor Pope says.
"While the operational structure supporting each kindergarten and teaching team will change, what happens each day at kindy for children, their family and whānau will continue."
He Whānau Manaaki president Amy Weighton said she saw the move as a positive step forward.
"We want kindergartens to be well supported in each community, with highly professional teaching teams and kindergarten staff offering fantastic experiences for every child."
He Whānau Manaaki will be holding its annual general meeting in Whanganui this
year.
The kindergarten amalgamation follows an announcement YMCA Central, which runs services in Whanganui and Palmerston North, will be merging with the Greater Wellington YMCA in the coming months.