There was only a little achievement in the implementation of the Comprehensive Peace Agreement or CPA.
National Security Minister in the Office of the President Oyay Deng Ajak said the border still remains undemarcated and the Abyei issue unresolved, Bakhita Radio reported.
He said South Sudan with no clear border demarcation poses a big threat to its citizens.
Mr Deng said the SPLM leadership were divided over the issue of popular consultation and the rights of self-determination.
He said the SPLM agreed to respect the rights of popular consultation to unite the people Southern Blue Nile and Kordofan.
Mr Deng warned that many countries still pose a lot of threats to South Sudan.
He made the remarks while opening national security policy consultations on Tuesday in Juba.