From what I think, the warehouse manager is not independent and so he should not be in charge of the audit
What about the other warehouse staff? Can they be involved in the counting of inventory ? If not, why not and who would then be responsible for counting the inventory/
Generally, you need warehouse staff involved with,stockcounts because they know what they are counting. However, they have incentive to cover up errors in stock amounts. The best arrangement is to have a mixed team, one person from the warehouse, one from accounts or internal audit.