Cycling Ireland voted 91-74 against endorsing McQuaid at an hour-long extraordinary general meeting in Dublin, leaving the Irishman to rely on his much-criticized nomination for the UCI presidency by the Swiss cycling federation last month.
"As the result indicates, it was a very close call," said Cycling Ireland chief executive Geoff Liffey, speaking after a vote made by representatives of 60 Irish clubs.
McQuaid's future as the head of world cycling's governing body — a position he has held for eight years — has been clouded since the U.S. Anti-Doping Agency report last year which led to Lance Armstrong being banned for life from cycling and stripped of his seven Tour de France titles.
USADA said the UCI helped cover up some suspicious samples from the American. Although McQuaid has denied any collusion, his reputation has still been tarnished and he has been accused of closing his eyes to the endemic doping culture in the sport.
Praise for his role in introducing the biological passport, which monitors an athlete's blood profile over time to look for signs of cheating, is wearing thin.
McQuaid is facing a fight for re-election in September, with Brian Cookson — the head of British Cycling — announcing this month that he will challenge for the UCI presidency.
McQuaid's endorsement by Swiss Cycling is also the subject of a legal challenge from three of the body's members.