The daily newspaper Tages Anzeiger said that Switzerland's Federal Intelligence Service had been tipped off by a western counterpart which intercepted the men's phone calls.
Switzerland's national prosecutor's office has confirmed the arrests but declined to give further details.
The newspaper said that the Swiss were informed that the three men were believed to have formed a pro-Isis cell.
"There were indications that the trio planned an attack in their adopted country," Tages-Anzeiger said, without elaborating.
The men's arrests were revealed on Sunday by the weekly newspaper NZZ am Sonntag, which reported that they were suspected of providing IS with logistical and financial support.
They allegedly helped around 40 Swiss or Swiss-resident jihadists travel to the Middle East to join IS.
According to the Tages-Anzeiger, known for its contacts within Swiss officialdom, the three Iraqis aimed to procure explosives and toxic gas for an attack.
It was not clear how far their alleged plans had advanced, the newspaper added.
It said that the men were aged between 28 and 33, and that at least one was an asylum seeker.
Two had lived in the northern Swiss regions of Aargau and Schaffhausen, which border Germany, while the listed address of the third man was in the Syrian capital, Damascus, the newspaper said.
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