Putin, currently prime minister, will be inaugurated for his third non-consecutive term Monday.
Election monitors in December suggested State Duma elections were skewed in favor of Putin's political party, United Russia. Similar concerns were expressed in a March election that secured a Putin's third term in office.
Yelena Panfilova, director of Transparency International Russia, and political analyst Dmitry Oreshkin are among those resigning from the presidential Human Rights Council.
"I regard Putin as an illegitimate president," Oreshkin was quoted by Russia's state-run news agency RIA Novosti as saying. "I won't be able to work in his council."
Oreshkin drafted a report that said 14 percent of the ballots in the March election were stuffed in Putin's favor. The report was rejected by the presidential council.
The presidential council has no legal authority. Several members resigned in the wake of State Duma elections in December.
Putin announced last month he would resign as chairman of his United Russia party before his inauguration.