At an extraordinary meeting of the Liberals in Geneva, the party base narrowly backed Maudet, despite formal requests from both the national and cantonal leadership for him to quit.
Maudet, who was forced to step aside from his role as cantonal president last September but remains head of the security ministry, is currently being investigated by Geneva state prosecutors over allegations he accepted financial benefits in relation to a 2015 trip to Abu Dhabi.
Last week, prosecutors also announced they wanted to broaden the scope of their investigation to look at whether Maudet – once considered a golden child of the Swiss political scene – also received benefits from Geneva hotel chain Manotel.
Before Tuesday's meeting, the local party leadership had called on members to force Maudet's resignation, arguing that his continued presence in the government was causing huge political damage.
The issue was political, not judicial, said cantonal party president Alexandre de Senarclens.
But Maudet on Tuesday set himself up as a victim of a campaign by the party leadership and the media, according to Swiss daily NZZ. He admitted he had made grave errors but told party members the trip to Abu Dhabi had not cost local taxpayers any money.
He had always had the best interests of the canton at heart, he said.
Maudet has repeatedly said that any decision on his part to resign would depend on the outcome of any criminal investigations.
The decision by the voters to back Maudet now means de Senarclens must step aside as cantonal party president. The Liberals in the canton of Geneva remain in crisis.