Human Rights Watch, CARE International and Refugees International were among the signatories of the appeal launched ahead of elections to fill 14 seats at the 47-nation council on Friday.
Russia, Hungary and Croatia will be running for two seats representing the Eastern European group at the council, which is tasked with addressing rights violations worldwide.
The organizations urged UN member states to "question seriously whether Russia's role in Syria -- which includes supporting and undertaking military actions which have routinely targeted civilians and civilian objects -- renders it fit to serve on the UN's premier inter-governmental human rights institution."
On Friday, the UN General Assembly will cast ballots to elect the members for a three-year term beginning in 2017.
Other than Russia, China and Saudi Arabia are almost guaranteed to win seats as their regional grouping is putting forward a clean slate of four countries for four seats. The other two are Iraq and Japan.
Brazil, Cuba and Guatemala will be battling for two seats representing Latin America.
Africa is also presenting a clean slate, with Egypt, Rwanda, South Africa and Tunisia set to win seats.
Created in 2006, the rights council monitors violations and in particular set up a ground-breaking commission of inquiry on North Korea that led to calls for war crimes prosecutions of the Pyongyang regime.
The council last week asked the commission of inquiry for Syria to carry out a special investigation of rights abuses in Aleppo.
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