The parenting education classes for newborn to five years old have been going since 2004.
The PEPE courses will finish at the end of June, resulting in the disestablishment of five permanent and 17 casual roles.
A further 16 people will have their hours reduced.
Chief executive Amanda Malu said the charity can no longer afford to run the programme at its current deficit of $400,000 a year.
"Like any charity that relies on donations and grants, we have limited resources. We are having to make this tough decision now to ensure that we remain financially resilient for the years ahead. Whānau Āwhina Plunket turns 115 next month and we want to make sure we are here for another 100 years."
She said it was a difficult time for staff affected by the decision.
"This is a sad day for Whānau Āwhina Plunket. We are proud of our staff and the work they have done for whānau and communities, and we know this programme will be missed.
"I would like to thank everyone who have been involved in PEPE over the years and acknowledge what a tough time this is - for the people who have been directly impacted, as well as their managers, colleagues, whānau and communities."
Facilitators have been running 600 courses each year attended by about 4000 parents and caregivers. Since Covid-19 the classes have been run online.
Malu said Plunket would continue to offer a range of other assistance.
"As part of our Ministry of Health-funded Well Child Tamariki Ora service, we also offer additional group sessions to parents who need extra support. Run by our Kaiāwhina and Community Karitāne, these groups are directly targeted at whānau who have been identified by our nurses as needing more help."
The groups would focus on common parenting issues such as breast-feeding, nutrition and starting solids, and sleeping and settling.
She said Plunket would continue to support parents and whānau through local community support and specialist referral services, by providing information on its website and through its regular educational Facebook live chats.
There are also plans to produce a series of educational video resources, which would be available free of charge on the website.
No other Plunket services are affected by this decision, including the Well Child Tamariki Ora service funded by the Ministry of Health.
