Maj. Darryl Watts faces six charges, including manslaughter, in the incident which killed Cpl. Josh Baker and injured four others in February, 2010.
The soldiers were peppered with ball bearings fired by a C19 Claymore anti-personnel mine on a training range north of Kandahar city.
Watts is accused of not ensuring the safety of his men even though he says he had no experience on the Claymore mine and turned the responsibility over to his second-in-command.
The judge in the case is allowing the jury to set its own hours, so it wasn't clear if deliberations were still underway Sunday night after the jury spent just 90 minutes behind closed doors on Saturday.
The jury will remain sequestered at a Calgary hotel until it reaches a verdict.