diff --git a/erpnext/setup/doctype/employee/employee.py b/erpnext/setup/doctype/employee/employee.py
index ead82ef8bf3..b4eb03fcbc6 100755
--- a/erpnext/setup/doctype/employee/employee.py
+++ b/erpnext/setup/doctype/employee/employee.py
@@ -53,7 +53,7 @@ class Employee(NestedSet):
 				user = frappe.get_doc("User", existing_user_id)
 				validate_employee_role(user, ignore_emp_check=True)
 				user.save(ignore_permissions=True)
-				remove_user_permission("Employee", self.name, existing_user_id)
+				remove_user_permission("Employee", self.name, existing_user_id, ignore_permissions=True)
 
 	def after_rename(self, old, new, merge):
 		self.db_set("employee", new)
@@ -91,11 +91,11 @@ class Employee(NestedSet):
 		)
 
 		if employee_user_permission_exists and not self.create_user_permission:
-			remove_user_permission("Employee", self.name, self.user_id)
-			remove_user_permission("Company", self.company, self.user_id)
+			remove_user_permission("Employee", self.name, self.user_id, ignore_permissions=True)
+			remove_user_permission("Company", self.company, self.user_id, ignore_permissions=True)
 		elif not employee_user_permission_exists and self.create_user_permission:
-			add_user_permission("Employee", self.name, self.user_id)
-			add_user_permission("Company", self.company, self.user_id)
+			add_user_permission("Employee", self.name, self.user_id, ignore_permissions=True)
+			add_user_permission("Company", self.company, self.user_id, ignore_permissions=True)
 
 	def update_user(self):
 		# add employee role if missing