The reformed protestant churches in 2014 counted 1.74 million members aged 15 and over, 87,000 less than in 2011, the federal statistics office (FSO) said in a report released on Thursday.
In 1970, one half of the Swiss population was protestant.
But in 2014, that share dropped to 25.5 percent, down from 27.8 percent in 2011, the FSO said.
The Roman Catholic church, which has the largest group of parishioners in the country, also saw its share of members drop to 37.9 percent of the adult population in 2014 from 38.4 percent.
However, its membership grew slightly to reach 2.59 million, the report said.
Both the protestant and Catholic churches have lost members to other faiths and to those without religious conviction.
Almost one in four people (23 percent) said they belong to no church, double the amount in 2000.
According the latest census, 5.7 percent of the population said they belonged to a Christian church other than protestant or catholic, while 0.2 percent declared themselves to be Jewish.
The Islamic community, meanwhile, accounted for 5.1 percent of the adult population in 2014, up from 3.6 percent in 2000.