The council-owned Willows Centre for Children in North End is set to shut in March with its 48 special educational needs and disability (SEND) children transferred to the Cliffdale Primary Academy (also a SEND school) on the same site.
The Willows Centre caters for children aged three to five.
Portsmouth City Council said the merger is vital to keep special needs places for younger children in the city.
In a report ahead of next week's education meeting Caroline Corcoran, from the council'sÂ education service, said: '˜Willows Centre for Children is a good school providing good quality education, but as a very small school it faces increasing financial uncertainty.
'˜There is a continuing need for specialist nursery places in Portsmouth and the proposal would safeguard the future of the provision which would be provided going forward by Solent Academies Trust.'
Although the pupils and staff will continue to be based in the same building on Battenburg Avenue it was clear that many were concerned Willows would '˜lose its identity'Â as a result of the move.
In the council consultation a Willows staff member said: '˜It is a shame to close Willows as it has a very strong reputation and is close to many parents'Â hearts. Can we keep its identity?'
Their colleague agreed. '˜The proposal fills me with sadness and trepidation,'Â they said.
'˜The contribution Willows has made to the lives of many vulnerable children and families is immeasurable. By closing Willows, the security net offered by a smaller, more user friendly school will be lost forever.'
A parent added: '˜Having been lucky enough to have a son that benefitedÂ hugely from attending Willows, I think it is a huge loss to the city that such a great nursery is closing.
'However, the changes are necessary to continue the great support given to SEND children and their education.'
Seven staff members and six parents said they were against the merger, but one worker and five parents supported it.
For the council's head of education, Cllr Suzy Horton, the academy will still provide the best service possible. '˜It won't be called Willows any more but I want to reassure people it will still carry on the professional service,'Â she said.
'˜I understand why the change would be difficult for staff as well because not only are they having to amalgamate with another school, but they're having to become an academy. But the priority is the students.'
Cliffdale Primary Academy will have its age range extended to accommodateÂ the new students.
The Willows day centre Catkins, which is not for SEND children,Â will close for good in July.