According to a statement released by the conference of governments of Western Switzerland (WRK), universities in Romandie have seen a reduction in enrolments by European students of between 11 and 38 percent compared with the autumn semester last year as a direct result of the "negative effects" of the referendum.
Even Switzerland’s two best known universities – the federal institutes of technology in Lausanne and Zurich – have suffered, with European student numbers down 10 percent at EPFZ and 14.4 percent at EPFL.
The university of Bern reported 11 percent fewer European students this semester, and Basel university also noted a reduction, without releasing an exact figure.
The only exception is the university of Zurich, whose EU student numbers were up by seven percent, a situation the institution is at a loss to explain, according to ATS.
Europe-wide student mobility programme Erasmus allows students throughout Europe the chance to spend a year studying in another European country.
Switzerland’s exclusion from the programme came after the February 9th referendum which gave the green light to a proposal to introduce immigration quotas within the country.
The proposal contravenes Switzerland’s bilateral agreement with the EU over the free movement of people within Europe.
As a result, the EU retaliated by excluding Switzerland from Erasmus as well as several high profile European research programmes.
In April the Swiss federal government launched an interim solution to allow continued student exchange by giving funds directly to Swiss students who want to study abroad and foreign students wishing to come to Switzerland.
The solution aimed to provide continuity for students while the government lobbied the EU for Switzerland to rejoin Erasmus.
But the solution is no substitute for the real thing, feels WRK.
"Although the confederation has put in place an interim solution for Erasmus... the instability surrounding Swiss participation in these programmes has led to a decrease in exchanges," said WRK president Alain Ribaux in a statement.
"International exchanges, amongst students as well as in collaborative research, are very important for our higher education establishments. In order to remain competitive and attractive, they need to pursue cooperation with European partners."
"International influence is a benefit not only for universities but also for university towns and the country as a whole."
In mid-September the government announced an extension of its interim solution for the next two years.
A budget of 23.6 million francs will be allocated for 2015 and 25.1 million francs for 2016 to allow continued student exchange between Switzerland and the EU.
The Swiss government has three years from the referendum date to decide how it will proceed with the introduction of as-yet unspecified quotas on immigration.
This week it launched a campaign against a proposal by environmental party Ecopop to limit immigration to 0.2 percent of the population, which would reduce immigrants to 17,000 a year from the current average of 80,000.