The proposals would merge Charlotte Sharman Primary School, which has no religious character, with St Jude's Church of England Primary School.
The resulting school would have a Church of England religious character.
The plans follow falling pupil numbers at both schools, although Charlotte Sharman is the larger of the two schools and has more places filled.
In a letter to cabinet member for children, education and refugees Councillor Jasmine Ali, the NSS said the merger would "significantly diminish parent's choice" to educate their child in an inclusive community school.
Charlotte Sharman is the only nonreligious school in the St George's ward of the London borough Southwark.
The letter pointed to the duty of local authorities to secure diversity in the provision of schools under the Education Act 1996.
It said the local community would be "ill served" by a new CofE school which can legally discriminate on the basis of religion in its admissions and hiring.
The letter cited St Jude's collective worship policy which requires children to pray twice a day.
St Jude's admissions policy explicitly privileges families that are "faithful and regular worshippers" at St George the Martyr and other Anglican churches.
The NSS noted the CofE is "strongly motivated" to support the merger as part of its plan to double the number of young "Christian disciples" by 2030.
The letter also raised "serious concerns" about consultation documents provided on the merger. It said they omitted "vital information" about the nature of faith schools that would leave parents and teachers "unable to make an informed choice".
The documents make no mention of faith-based admissions and hiring, legally mandated collective worship or faith-based religious education.
The NSS said the documents make "no attempt" to justify why the resulting school should be CofE and instead issue a "summary judgement".
It said the decision was "especially perplexing" given both schools are minority Christian.
Furthermore, St Jude's has filled only 39% of its places compared to Charlotte Sharman's 78%.
The letter urged Ali to "preserve the secular ethos" of Charlotte Sharman or any new school resulting from a merger.
A petition set up by Southwark National Education Union to defend the secular ethos of Charlotte Sharman has attracted over 700 signatures.
It notes Charlotte Sharman "serves the diverse community" of Elephant and Castle and is "an inclusive, community school" without any emphasis on any particular religious belief.
NSS: 'Council must serve needs of children and families not agenda of the Church'
National Secular Society chief executive Stephen Evans said: "Any proposal that strips a religiously diverse community of an inclusive secular school and forces children into a Church of England school defies logic and fails to respect the principle of freedom of religion or belief.
"Southwark Council must ensure it is first and foremost serving the needs of local children and their families – not the agenda of the Church.
"In a pluralistic and increasingly secular society, there should be a presumption towards religiously neutral schools to ensure students from all backgrounds can feel equally welcome and valued and not have other people's religion imposed on them."