NWC chairperson Gráinne Healy said the council had taken this decision because the Sustaining Progress agreement does not progress equality among women.
"It makes no genuine attempt to address the needs of the marginalised or socially excluded those whose voices are outside the employed and employing classes," Ms Healy said.
The National Women's council, which represents 169 organisations nationwide, entered the national negotiations with a range of proposals.
These included demands for: Increased childcare provisions; Increased women's representation in decision-making; Poverty among women to be tackled.
The NWC wanted the Government to agree to annual targets of increased childcare places, but their demands were not met.
The council also wanted social welfare benefit be benchmarked to increases in the average industrial wage. However, that proposal was not accepted by the Government either.
"Adequate income and social inclusion are basic human rights and a document which fails to acknowledge this fact is not a document the NWC can endorse," Ms Healy said.
The NWC's negotiator, Orla O'Connor, said the new agreement is just a restatement of Government commitments.
Ms O'Connor said it offered no new resources to achieve equality for women and was basically just an 18-month pay deal.
Sustaining Progress has no new targets, time scales or specific commitments to bring about change for those living poverty and experiencing inequality in our society, Ms O'Connor added.
The council is now calling on all other organisations representing those who are experiencing inequality not to accept this agreement.
"Achieving equality for women must be the central goal in the development of Irish society," Ms O'Connor said.