Federal Prosecutor Valentin Roschacher says Switzerland was probably used as a base for the financing and logistical support of al-Qaeda.
His comments come as the Swiss authorities prepare to begin legal proceedings in three terror cases launched in the wake of the September 11 attacks.
At a press conference in the Swiss capital, Bern, Roschacher denied that Switzerland was a major hub for militant groups.
"Switzerland has so far not played a central role as a location for the activities... of al-Qaeda," said Roschacher.
"But it is suspected that offences in logistical and financial support have been committed in the country."
The Federal Prosecutor's Office confirmed that three cases linked to suspected terrorist activities in Switzerland would be handed over to an investigating judge, who will decide whether to launch court proceedings.
One of the Swiss investigations is centred on Al-Taqwa Management, a financial firm which was based in Switzerland until it went into liquidation in December 2001.
The United States has accused the company of helping to fund Osama bin Laden’s network.
List of names
Al-Taqwa was founded in 1988 and was run from Lugano in canton Ticino by its Egyptian-born managing director, Youssef Nada, and his Syrian-born associate, Ali Himat.
The company is on Washington’s list of organisations accused of helping to fund terrorism.
Soon after the list was published Swiss police raided the firm’s headquarters in Lugano.
The company’s bank accounts as well as those belonging to its board members have since been frozen.
Officials at the firm have repeatedly denied links to terrorism and accused the authorities of taking part in a US-led anti-Muslim campaign.
A second investigation has focused on a businessman from Saudi Arabia who allegedly acted as a point man for al-Qaeda, with ties to Switzerland and the US.
The unidentified man is believed to have used Swiss accounts to transfer millions of francs to individuals connected with al-Qaeda.
A Geneva bank account containing around $20 million (SFr24.8 million) has been frozen as part of the investigation.
A third investigation centres on the alleged ties of a number of Swiss-based foreign nationals to a series of bombings on residential compounds in the Saudi Arabian capital, Riyadh, in May 2003.
Thirty-five people were killed in the attacks, including one Swiss citizen.
Swiss police have arrested ten foreigners in connection with the attacks. Six are still being held in custody.
Court documents revealed that the authorities based their investigation in part on numbers stored in mobile telephones found in Saudi Arabia.
Investigators have also uncovered evidence that some of the al-Qaeda members who struck the US on September 11, 2001, made calls in Afghanistan and Pakistan using phones with prepaid phones bought in Switzerland.
The Swiss government announced on Wednesday that as of August 1 it will no longer be possible to purchase a prepaid mobile without providing proof of identity.
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About $20 million (SFr24.8 million) of funds have been blocked in a Geneva bank account.
Since September 2001 the Swiss justice authorities have folllowed up more than 1,000 tips about possible links between Switzerland and the al-Qaeda network.
Ten people were arrested in Switzerland in connection with an investigation into bomb attacks in Riyadh in May last year.
Six of the ten suspects are still being held in custody.
The individuals were arrested on suspicion that they helped citizens of Arab nations enter Switzerland illegally and provided them with fake identities.