The Council of Europe resolution urged its 47 member states to ensure the latest medical and sanitary conditions are met during ritual circumcisions, which are often performed on boys at an early age in Judaism and Islam.
It called for "dialogue between... medical doctors and religious representatives, so as to overcome some of the prevailing traditional methods, which do not take into consideration the best interest of the child and the latest state of medical art."
Ritual circumcisions in Judaism, Israel's dominant religion, are usually carried out by a religious official specialised in the practice.
The Israeli foreign ministry criticised the resolution, which passed by 77 votes to 19 with 12 abstentions on Tuesday, saying it fostered "racist trends".
"After the Parliamentary Assembly of the Council of Europe (PACE) adopted a resolution against circumcision, Israel calls on the Council to rescind immediately the resolution," the ministry said.
"Claims that circumcision harms young boys? health and body are false, and do not rest on any scientific evidence," it added.
"This resolution casts a moral stain on the Council of Europe, and fosters hate and racist trends in Europe."
Israel took particular exception to PACE's adoption of a single resolution dealing with both female genital mutilation and the circumcision of young boys on religious grounds.
"Circumcision of male children is an ancient religious tradition.... Any comparison of this tradition to the reprehensible and barbaric practice of female genital mutilation is either appalling ignorance, at best, or defamation and anti-religious hatred, at worst," the ministry said.
But the PACE rapporteur who put forward the text, Marlene Rupprecht, rejected the criticisms, saying the resolution "in no way compares the circumcision of boys to female genital mutilation".
"We did mention different categories of violation of the physical integrity of children, which we, however, very clearly distinguished and did not mix up in any way," she said in a statement issued on the council's website.
The text "does not intend to stigmatise any religious community or its practices", she said.
"On the contrary, the assembly calls for public debate aimed at reaching a wide consensus on the rights of children to protection against violations of their physical integrity."
"It is the Council of Europe's mandate to promote the respect for human rights, including children's rights, on an equal footing with the fight against racism, anti-Semitism and xenophobia," said Rupprecht, a German social-democrat parliamentarian.
The council's Parliamentary Assembly meets for a week four times a year, and brings together 318 parliamentarians from 47 countries.