The Islamic Central Council of Switzerland (ICCS), in a statement, affirmed "full support for (board member) Naim Cherni" and said his work "in no way has anything to do with Al-Qaeda."
Cherni was not named in a statement on Saturday from the Swiss attorney general, which said that an ICCS board member was being probed for violating "the prohibition of groups like Al-Qaeda, Islamic State (Isis) and similar organizations."
The German national is suspected of making a video "for propaganda purposes" with material collected from a trip to war-ravaged Syria, according to the Swiss attorney general.
Prosecutors made specific reference to interviews in the video with a fighter who reportedly has ties to an Al-Qaeda affiliate.
Switzerland's ATS news agency said Cherni also defended himself at a press conference in Bern on Monday, saying his reason for repeatedly travelling to Syria was to document the civil war.
The announcement of the criminal probe came after the Swiss government said it was significantly boosting the wealthy Alpine nation's counter-terrorism forces, amid a heightened security alert in the wake of the November 13th attacks in Paris that left 130 dead.
Authorities in Geneva have since last week been searching for possible extremists with links to the Isis group, with reports that US intelligence had identified a jihadist cell in the city.