Swiss-born Infantino was elected Fifa president in February 2016 and had been expected to sweep to a fourth and final term at elections next March, until a failed bid to allow private investment in the World Cup drew calls for reform.
The Swiss Football Association (ASF), one of Fifa's founding members in Paris in 1904, said in June that it would support Infantino.
However, it has gone back on the pledge following a meeting of its central committee on 25 September.
"From the ASF's perspective, several events raise fundamental questions regarding leadership, governance, transparency and decision-making processes within Fifa," said a statement issued on Wednesday.
"This relates in particular to issues of clarity of rules and the integrity of competitions."
Swiss football administrators said they were concerned over the way that Fifa allowed United States President Donald Trump to interfere with the 2026 World Cup in the US, Mexico and Canada .
Trump revealed he had contacted Fifa and urged it to suspend a one-match ban on US striker Folarin Balogun for his red card during the United States' 2-0 victory over Bosnia and Herzegovina on 1 July. The penalty was lifted the day before the Americans played Belgium for a place in the quarter-finals.
The ASF also cited the way Infantino presented his plan to create a commercial company , Fifa Forward Enterprise, to run the World Cup and other events.
Under the scheme, Infantino proposed spinning off commercial and operational rights of Fifa competitions – including World Cups and Club World Cups for men and women – into a €17 billion subsidiary, with 20 percent owned by private investors including the Kushner family, which has links to Trump.
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"For the ASF, credibility, transparency, accountability and the effective involvement of the relevant bodies in accordance with the statutes are essential prerequisites for confidence in the governance of international football and in Fifa's integrity," the ASF added.
"In view of the developments since June 2026 and the outstanding issues, the ASF central committee considers that these conditions are no longer met."
In September, the football federations of France and Belgium withdrew their backing for Infantino.
The Belgian federation said it also wants the Balogun case to be discussed at the next meeting of the Fifa council on 15 October in Zurich, Switzerland.
Both Fifa and European football's governing body Uefa are based in Switzerland.
ASF president Peter Knabel said the Swiss association expected Fifa's leadership to uphold the highest standards of transparency, accountability and institutional responsibility.
The Swiss move comes a week before top Uefa executives meet in Berlin.
They are expected to discuss the widening rift with Fifa over Infantino's leadership and possible challengers to the president, who retains support from the African and South American football federations.
He also has the backing of 2034 World Cup hosts Saudi Arabia .
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On Tuesday, Nasser Al-Khelaifi, the president of the European champions Paris Saint-Germain , ruled himself out as a possible contender to topple Infantino.
Speaking in Copenhagen after the annual meeting of the European Football Clubs , Al-Khelaifi said: "I have zero interest in Fifa. I have zero agenda or ambition to be there.
"I don't think I'm the right guy for this position and I don't want to go actually. I'm enjoying what I'm doing."
Under his stewardship since 2011, PSG have harvested 43 pieces of silverware including 12 Ligue 1 titles and seven Coupe de France trophies. PSG won the Champions League for the first time in 2025 and in May became only the second team after Real Madrid to win back-to-back crowns since the Champions League morphed out of the European Cup in 1992.
Nominations for Fifa's presidential election next March must be submitted by 18 November. Infantino is the only candidate so far.
