She says the document places restrictions in the name of "regional and national particularities", and creates requirements such as the balancing of rights and duties.
"They have to adhere to the universal standards adopted by all states under the UN charter," Ms Pillay told Radio Australia's Asia Pacific at the close of the Bali Democracy Forum.
"But these lapses in this document are not in line with international standard and as I have stated many times, regional human rights instruments can and should enhance and complement the international human rights system."
Ms Pillay says she has called on the governments of ASEAN to consult broadly with civil society before adopting the current draft of the Declaration.
She says the current draft of the Declaration has not yet been published.
Burma concernsMs Pillay says she met with Burma's Deputy Foreign Minister at the Forum to discuss the human rights situation in Rakhine state.
"[I] urged that Myanmar should show more concern for the suffering and loss of life in the communities impacted by the violence there," she said.
"If the communal violence is not resolved it can undermine the reform process in Myanmar.
"One of the underlying causes of the violence since June between communities in Rakhine state is the endemic discrimination against the 800,000 Rohingya."
Ms Pillay says leaders who visit Burma should not just have bilateral discussions but also make "a public statement on where they stand with human rights violations."