They say the commander, named as Mirwais, was in charge of a 20-man checkpoint when he defected on Sunday.
The men are said to have taken heavy weaponry, radios and police vehicles including US-made armoured Humvees.
Farah is one of the most insecure areas in the relatively peaceful west.
The commander was based in Shewan village in the district of Bala Bulak, which was until recently considered a Taliban stronghold.
The insurgents were driven out of the area following a series of operations carried out by Afghan security forces. But local officials say insurgents have regrouped in the area recently.
CONTINUED at BBC News.