The organisation called on Greek MPs to reconsider the bill, which will boost the power of police to order deportations and detain undocumented migrants while strictly regulating the activities of NGOs and volunteer groups.
Greece is still a major hub for migrants trying to reach the European Union, though arrivals are far lower than they were during the peak of the migrant crisis in 2015.
The Greek government has defended the tough proposals as necessary to protect its borders.
"Greece will not accept, as in the period 2015-19, to be the gateway to Europe for illegal immigration flows," Migration Minister Notis Mitarachi told parliament earlier this week when he presented the bill, which MPs will vote on later on Friday.
However, the Council of Europe's rights commissioner Dunja Mijatovic said the plan "would seriously hinder the life-saving work carried out at sea by NGOs, and their human rights monitoring capacities in the Aegean".
The law allows for stiff fines and sanctions for groups found to have impinged on the jurisdiction of the authorities and coast guard.
She stressed that NGOs were instrumental in protecting the rights of migrants and play a major role in documenting pushbacks or other potential violations.
She urged MPs to make sure the law respected Greece's obligations under the European Convention on Human Rights and the Refugee Convention.
