The office of Switzerland's attorney general (OAG) refused to confirm to AFP that Huber was the target of the criminal probe opened in March 2018.
The OAG said only that the investigation was linked to "illegal mineral trade in the Democratic Republic of Congo during the Second Congo War," which ran from 1998 to 2003.
The investigation concerns "suspected violations of the laws of war," it added.
TRIAL International, a Swiss NGO, had in 2016 filed a complaint against Huber, accusing him of dealing with armed groups in mineral-rich eastern DRC during the conflict.
TRIAL has not seen the confidential Swiss investigation and could not independently confirm that Huber was the target.
A 2009 investigation mandated by the United Nations Security Council cited Huber more than 30 times, repeatedly identifying him as being involved in the transport of minerals out of DRC during the conflict.
The UN report said Huber had connections with several companies, including in Rwanda, a country that along with Uganda backed several rebel militias that fought in eastern DRC.
TRIAL said Huber is "suspected of having committed pillage in the Democratic Republic of the Congo, a war crime under Swiss law."
TRIAL added that it had documents and other evidence proving Huber worked with RDC-Goma, a Rwandan-backed rebel force.
AFP was not immediately able to contact Huber, who has not been charged with a crime.
TRIAL alleged that in 2001, a company represented by Huber "was granted a mining concession by RCD-Goma."
"The concessions did not last long, but he was still able to acquire tons of cassiterite and wolframite during the time when he held concessions," said TRIAL in a joint statement with the New York-based Open Society Justice Initiative.
"Too many conflicts around the world are fuelled by the illegal sale of pillaged resources into global markets. Yet the international businesses and business people involved are rarely, if ever, prosecuted," said Ken Hurwitz of the Open Society Justice Initiative.
He "applauded" the Swiss for tackling "this complex and important case."
Millions of lives were lost in the 1998-2003 conflict, which also saw Ugandan and Rwandan troops enter Congolese territory.
Eastern DRC has been devastated by waves of violence, much of it blamed on rival militia, since the conflict.