President Jacob Zuma.
The Council for the Advancement of the South African Constitution has asked the highest court in the land to force Zuma to make the appointment within 30 days.
Read: President Zuma's conflict of interest
Beeld reported on Thursday that President Jacob Zuma's legal team on Wednesday informed the rights group in writing of Zuma's decision to oppose the application.
The prosecuting authority has been headed by acting head Nomgcobo Jiba for the past 18 months, but has been without a permanent head since the Supreme Court of Appeal set aside Zuma's appointment of advocate Menzi Simelane as NDPP in 2011.
The presidency has to submit its response to the court by July 19.
Zuma has been criticised heavily for not appointing someone to the position, especially after corruption charges against him were dropped by the NPA even though reports suggested that prosecutors were overwhelmingly in favour of going ahead with charges against him.
The charges were dropped against Zuma before he was chosen as president, and the controversial spy tapes were dismissed by the NPA.
Last year, the parliamentary oversight committee on justice said it was concerned about the length of time it has taken to appoint a head to the NPA, saying that alleged criminals like Radovan Krejcir, Andrew Phillips and Glenn Agliotti escaped prosecution because there is no national director of public prosecutions.
But Deputy Minister of Justice Andries Nel said he was not a concern as the NPA had other representatives in the structure, including four national deputy directors of prosecution, nine provincial directors and over 3 000 prosecutors.
The current acting NDPP, Jiba, has her own controversies. She was suspended from a senior position in the National Prosecuting Authority four years ago by its then-head, Mokotedi Mpshe, after facing internal charges of unprofessional conduct, dishonesty, fraud and bringing the NPA into disrepute. – Additional reporting by Sapa