Sweden's Armed Forces have confirmed the information for Sveriges Radio.
The officer is one of the Swedish military's most experienced soldiers when it comes to international missions.
He's led forces in Afghanistan in 2002 and one year later was the highest ranking Swedish officer in the Democratic Republic of Congo.
Now he is back in Africa, leading Swedish force deployed to Chad who once again are under French command.
In the Congo, French soldiers are said to have tortured a young Congolese man at the Swedish-French camp of Chem chem.
According to the Svergies Television investigative news program Uppdrag Granskning, Swedish soldiers tried in vain to get their commander to stop the torture.
The officer is also accused of having suppressed a report from one of the soldiers under his command.