A full 78.4 percent of voters embraced changes made to the asylum law last September as applications soared to their hightest level in over a decade.
Opponents of the asylum law revision, which includes the removal of military desertion from a list of valid grounds for seeking asylum in Switzerland, voiced deep disappointment at their defeat.
"The referendum is a disaster for asylum seekers and refugees and leaves no winners," the committee that had requested the vote on the changes said in a statement, hailing the "minority of the population that still has a conscience".
Manon Schick, the head of Amnesty International's Switzerland section, also lamented the "very, very high" percentage of Swiss who had voted in favour of the revision.
"We knew in advance that we would lose," she told AFP, pointing out that the Swiss have repeatedly voted to tighten their asylum law since it went into effect in 1981, "but that it was this bad was very disappointing."
Céline Amandruz of the populist Swiss People's Party (SVP), however welcomed the strong support for the tougher law, insisting that nine out of 10 people who seek refuge in the wealthy country did so "for economic reasons".
"There is clearly a need to change this system," she said.
One of the most controversial revisions was the removal of military desertion as a valid reason for asylum.
That has been the key reason cited by Eritreans, who accounted for most applications to Switzerland last year and whose country imposes unlimited and under-paid military service on all able-bodied men and women.
The revision also removed the possibility, which had been unique in Europe, to apply for asylum from Swiss embassies -- a change opponents described as "inhumane", since it meant people unable to make the often dangerous journey from their country to Switzerland would remain without help.
Justice Minister Simonetta Sommaruga has insisted that the changes largely benefit the asylum seekers themselves, highlighting especially the efforts to speed up the application process.
"Leaving people and their families for so long wallowing in uncertainty is unacceptable," she said recently.
The rejigged asylum law also clears the way for the creation of special centres for asylum seekers considered to be trouble-makers and limits the right to family reunification to spouses and children.
Many opponents complained Sunday that Sommaruga had mixed harsh tightening measures in with the legitimate change of shortening the application handling process — which can drag on for years.
"I don't believe 80 percent of Swiss voters said yes because they are xenophobic," Schick said.
Switzerland currently counts some 48,000 people in the process of seeking asylum, including 28,631 who arrived in 2012.
The surge, attributed in part to the Arab Spring uprisings, marks the highest number since the height of the Balkans war in 1999, when nearly 48,000 people sought refuge in the country.
Switzerland counts one asylum seeker for every 332 inhabitants, trailing only Malta, Sweden and Luxembourg, and ranking far above the European average of one asylum seeker for every 625 inhabitants.
Besides the asylum law, the Swiss also voted on a series of other national, regional and local issues Sunday.
Among them was an initiative for the people to elect their government directly instead of it being chosen by parliament.
This was rejected by an overwhelming 76.3 percent of Swiss voters.
Other votes included one in Zurich, where voters embraced a bid to impose tougher measures against hooliganism.
Only 39 percent of the 5.2 million people eligible to vote meanwhile cast their ballot Sunday, but low turnout is not uncommon in Switzerland, which hosts numerous popular votes each year.
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