"Investigations are ongoing" regarding the Palais Coburg hotel, the location of numerous rounds of the talks including discussions this week, interior ministry spokesman Karl-Heinz Grundböck told AFP.
On Wednesday, Russian-based IT security firm Kaspersky has said that malware dubbed Duqu, which is a sophisticated spy tool that was believed to have been eradicated in 2012, appeared to have been used to spy on the nuclear negotiations.
The Swiss attorney general's office confirmed it had launched an investigation on May 6th and conducted a raid six days later, seizing computer equipment, due to "suspicion of illegal intelligence services operating in Switzerland."
It did not specify if hotels were targeted in the probe.
Karl-Heinz Grundböck said that at present there was no clue as to who was behind the alleged cyber espionage.
However, Austria's Kronen Zeitung tabloid reports that there has been speculation in Israeli media that the cyber attacks bore "the hallmark of Israeli intelligence operations".
Israel's Foreign Minister Tzipi Hotovely has rejected any involvement. "Foreign reports about Israeli participation are baseless", she told Israeli army radio on Thursday.
June 30th is the deadline for a historic agreement between Iran and world powers on curtailing Tehran's nuclear programme in return for relief from punishing sanctions.
The US State Department said it was confident there had been no security breach in the talks.
"We've taken steps throughout the negotiations to ensure that confidential details and discussions remain behind closed doors," spokesman Jeff Rathke told reporters in Washington.
A member of the Iranian negotiating team said its side had always been cautious about the risk of spying and had taken care to "preserve secrecy" during the talks.
"The Iranian negotiators have always taken account of the possibility and the significant risk of listening and spying and have always acted with caution" during the talks, said the unnamed official, quoted by the official IRNA news agency.