Sonko has been in custody since his arrest in January 2017 in Switzerland, where he had applied for asylum after being sacked as The Gambia's interior minister, a post he held from 2006 to 2016.
Following a criminal investigation lasting more than six years, the Office of the Attorney General of Switzerland (OAG) filed an indictment against Sonko in the Federal Criminal Court.
"The defendant is accused, in his various capacities and positions, of having supported, participated in and failed to prevent systematic and generalized attacks as part of the repression carried out by the Gambian security forces against all opponents of the regime," a government statement said.
"The charges cover a period from 2000 to 2016 and constitute, in certain cases, crimes against humanity," it added.
Jammeh held sway over the tiny West African state for 22 years until he was unexpectedly defeated in presidential elections in December 2016 by political newcomer Adama Barrow.
He then fled to Equatorial Guinea.
Sonko had been one of Jammeh's top aides, serving in his presidential guard before heading the interior ministry. He was fired in September 2016.
"The OAG accuses the defendant in particular of having, in the context of five events between 2000 and 2016, participated, ordered, facilitated and/or failed to prevent killings, acts of torture, acts of rape and numerous unlawful detentions," the prosecutors' statement said.
Since 2011, Swiss courts have been authorized to hear serious crimes allegedly taken place outside the country, provided that the accused is in Switzerland and cannot be extradited or handed over to an international criminal court.
Swiss Charge Jammeh Minister With 'Humanity Crimes'
FILE - Gambia's former leader Yahya Jammeh, in white, is seen at Banjul airport, Gambia. Taken Jan. 21, 2017.
GENEVA - Swiss prosecutors said Tuesday that they had filed a crimes against humanity charge against Ousman Sonko, who was interior minister in the government of Gambia's former dictator Yahya Jammeh.