German prosecutors said Thursday they had filed war crime charges against the alleged leader of a rebel group which fought in Syria alongside Islamic State jihadists.

Syrian Amer A., the suspected chief of the group Liwa Jund al-Rahman, is accused of war crimes in "the form of forced displacement, looting in two cases and destruction".

Prosecutors also charged another Syrian named as Basel O. for membership in the group and arrested a third suspect over similar crimes.

Amer A. is alleged to have founded the Liwa Jund al-Rahman in 2013 in the Syrian province of Deir ez-Zor and acted as its leader.

The rebel group aimed to "violently bring down the Syrian regime", aligning itself with the Free Syrian Army but following an "Islamist agenda", prosecutors said.

In June 2013, Amer A.'s fighters are said to have joined other jihadist groups in an attack on the eastern village of Hatlah that killed up to 60 Shiite residents.

Survivors were made to flee by Liwa Jund al-Rahman fighters "intentionally stoking fears of death".

The armed group also "took valuables and destroyed religious and cultural institutions".

The result was "the end of all Shiite presence in Hatlah", prosecutors said.

In 2014, Amer A. joined the IS jihadist group and placed his fighters and financial resources under IS authority, according to prosecutors.

Basel O. is alleged to have held "a prominent military position" in Amer A.'s organisation in 2013-2014.

The suspect commanded combat units that fought Syrian troops, notably at Deir ez-Zor's military airfield, prosecutors said.

A third Syrian man, Sohail A., was arrested on Wednesday on suspicion of belonging to Liwa Jund al-Rahman and the Islamic State.

Sohail A., who allegedly worked as a media officer, "created propaganda videos, including of the incident in Hatlah", prosecutors said in a separate statement.

He was also accused of war crimes for forced displacement.