Al-Bashir has consistently denied involvement in the crimes.
The new charges came on the same day the joint UN/African Union UNAMID peacekeeping force said that at least 221 people have died in fighting and other violence in Darfur in the month of June.
"After assessing security reports for the past month, UNAMID estimates the number of fatalities due to armed conflict and criminality in Darfur in June to be 221," UNAMID officials said in a statement.
Violence has spiked in the arid western territory since the Justice and Equality Movement (JEM) suspended its participation in negotiations in Qatar in early May.
The fighting, which first surged in 2003 when mostly non-Arab fighters took up arms demanding more autonomy, has persisted in the face of a series of failed ceasefires and diplomatic pressure from the United States and other powers.
The recent surge has been fuelled by an increase in clashes between government troops and opposition fighters, together with tribal tensions not directly linked with the conflict.
Nearly 140 of the June deaths were caused by long-running feuds between the rival Arab Rizeigat and Misseriya groups, UNAMID said.
May was Darfur's bloodiest month in more than two years with UNAMID reporting nearly 600 deaths in rebel and tribal fighting.