Charles Ellicott Commentary Numbers 31:6

"And Moses sent them, a thousand of every tribe, to the war, them and Phinehas the son of Eleazar the priest, to the war, with the vessels of the sanctuary and the trumpets for the alarm in his hand." — Numbers 31:6 (ASV)

With the holy instruments, and ... —Or, with the holy instruments, even, etc. It does not appear whether the ark did or did not accompany the expedition. It has been inferred from Numbers 14:44 that the reference may be to the ark, but it does not appear probable that the ark would be so described. Moreover, Phinehas was not the high priest, and therefore would not have the ephod with the breastplate, which was worn at this time by Eleazar. The reference may be only to the silver trumpets , or it may include other sacred instruments.

This was emphatically a holy war. We may learn, from the command given to the Israelites to take with them the holy instruments, that those who would engage in the war against sin and Satan must take to them the whole armour of God (Ephesians 6:13).