The auditing was scheduled to resume at 7 a.m., but the process began 40 minutes later with the participation of observers from presidential candidate Abdullah Abdullah's team, Xinhua reported.
The election commission had planned to resume the process on Saturday but suspended it until Sunday due to the absence of observers from Abdullah's team.
However, the process was resumed on Sunday afternoon in the absence of observers from Abdullah's team.
Nasrullah Baryali Arsalai, an aide to Abdullah announced on Sunday that auditing process in the absence of Abdullah's team had no legitimacy.
The auditing process of votes has been suspended five times since its start July 17.
The Afghan presidential runoff was held June 14, but the result is yet to be announced.