Israel and Swiss Jewish groups have criticised Moritz Leuenberger for speaking out against a boycott of the Hamas-led Palestinian government.
Leuenberger told the Arab news channel, Al-Jazeera, that it would have been more "reasonable" to grant Hamas a probationary period to prove itself.
This year's Swiss president was reacting to a decision by the European Union and United States to suspend direct aid to the Palestinian government.
In part of the interview, which was broadcast on Swiss television on Tuesday evening, Leuenberger said: "Democratic elections were held and one has to accept the results."
On Wednesday the Israeli ambassador to Switzerland, Aviv Shir-On, said Hamas had had enough time since its victory at the polls in January to recognise Israel and renounce violence.
Shir-On said he would meet Leuenberger in the "coming days" to present Israel's views on the issue.
The Swiss Federation of Jewish Communities echoed his response. In an open letter to Leuenberger, it accused him of being "naïve". "How much time should we give Hamas to recognise the state of Israel and stop supporting terrorism?" it asked rhetorically.
Leuenberger told Swiss television on Wednesday evening that the criticism was unjustified, adding that he had clearly denounced violence during the Al-Jazeera interview.
A spokesman for the Swiss foreign ministry, Jean-Philippe Jeannerat, said the president's comments did not alter Switzerland's position towards the Palestinian government in any way.
Switzerland does not provide the Palestinian authorities with any direct funding, but provides development aid.
Leuenberger's spokesman also defended the president, stressing that the comments aired on Swiss television were only part of a much longer interview.
swissinfo with agencies
Hamas is not banned in Switzerland.
The radical Islamic organisation won parliamentary elections in January with 76 of 132 seats.
Switzerland's support to the occupied territories consists mainly of development aid to the Palestinians.
This is provided through non-government organisations and other international groups.
The Swiss authorities provides no financial assistance, except for the statistics office.
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