The accused who is identified as Amanullah is a resident of Orgo District of northeastern Badakhshan province.
Lal Mohammad, spokesman for the police headquarters of Badakhshan province said that Amanullah was arrested by police during a raid.
Amanullah is one of the two soldiers who went missing from a security post in Shah Joy District of southern Zabul province on the night of September 6 when five soldiers in the same post were found dead.
Wazir Mohammad Jawadi, governor of Shah Joy District said that upon receiving information about the incident, they sent a team to the security post in Kajarkhil area and saw that five soldiers were martyred and two others missing.
He said that weapons were also gone missing from the security post.
These five were among the at least 30 soldiers who lost lives in similar attacks in southern Afghanistan since the beginning of August.