diff --git a/erpnext/accounts/doctype/accounts_settings/accounts_settings.py b/erpnext/accounts/doctype/accounts_settings/accounts_settings.py
index 9fc9854..5f569a8 100644
--- a/erpnext/accounts/doctype/accounts_settings/accounts_settings.py
+++ b/erpnext/accounts/doctype/accounts_settings/accounts_settings.py
@@ -16,7 +16,9 @@
 		if cint(self.auto_accounting_for_stock):
 			# set default perpetual account in company
 			for company in frappe.db.sql("select name from tabCompany"):
-				frappe.get_doc("Company", company[0]).save()
+				company = frappe.get_doc("Company", company[0])
+				company.flags.ignore_permissions = True
+				company.save()
 
 			# Create account head for warehouses
 			warehouse_list = frappe.db.sql("select name, company from tabWarehouse", as_dict=1)
@@ -25,4 +27,5 @@
 				frappe.throw(_("Company is missing in warehouses {0}").format(comma_and(warehouse_with_no_company)))
 			for wh in warehouse_list:
 				wh_doc = frappe.get_doc("Warehouse", wh.name)
+				wh_doc.flags.ignore_permissions = True
 				wh_doc.save()