The Swedish government authorized the prosecution authority to proceed with an indictment against Alex Schneiter, a Swiss national currently serving as chief executive of Lundin Oil (now known as Lundin Petroleum), and Ian Lundin, the company's Swedish chairman of the board.
“Given the severity of the crime, justice must be allowed to run its course,” Justice Minister Morgan Johansson said.
Sweden can prosecute crimes committed abroad in its court system, but the government's approval is needed to press charges against a foreign national for crimes committed abroad, a justice ministry spokeswoman told AFP.
The pair face a life sentence if convicted.
Lundin Oil is suspected of funding the Sudanese army and several militias to chase away local populations from regions where the company planned to carry out oil exploration.
According to aid organisations, oil activities in the politically unstable region of southern Sudan fuelled a conflict between Khartoum and rebels.
Aid organization Ecos said in 2010 that 12,000 people were killed or died of starvation, exhaustion or disease directly linked to the conflict between 1997 and 2003 in the area where Lundin Oil was active.
Swedish prosecutors opened a preliminary inquiry into the case in 2010.
In 2016, Schneiter and Lundin were formally suspected of being complicit to violations of international law, a term in the Swedish justice system that covers war crimes, crimes against humanity and genocide.
On its website, the oil group said it believes “there are no grounds for any allegations of wrongdoing by any representative of the company.”
“Lundin Petroleum strongly believes that it was a force for development in Sudan and was at all times an advocate for peace by peaceful means in the region,” it added.