diff --git a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.js b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.js
index bd906665398..f80126bcb0a 100644
--- a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.js
+++ b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.js
@@ -38,7 +38,7 @@ frappe.query_reports["Stock Qty vs Batch Qty"] = {
 				frappe.call({
 					method: "erpnext.stock.report.stock_qty_vs_batch_qty.stock_qty_vs_batch_qty.update_batch_qty",
 					args: {
-						batches: selected_rows,
+						selected_batches: selected_rows,
 					},
 					callback: function (r) {
 						if (!r.exc) {
diff --git a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.json b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.json
index b1885bb07f4..147815be88d 100644
--- a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.json
+++ b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.json
@@ -10,7 +10,7 @@
  "idx": 0,
  "is_standard": "Yes",
  "letterhead": null,
- "modified": "2025-10-07 20:03:45.952352",
+ "modified": "2025-11-18 11:35:04.615085",
  "modified_by": "Administrator",
  "module": "Stock",
  "name": "Stock Qty vs Batch Qty",
@@ -21,10 +21,7 @@
  "report_type": "Script Report",
  "roles": [
   {
-   "role": "Stock Manager"
-  },
-  {
-   "role": "Stock User"
+   "role": "Item Manager"
   }
  ],
  "timeout": 0
diff --git a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.py b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.py
index 4818f36610c..d88d610d23e 100644
--- a/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.py
+++ b/erpnext/stock/report/stock_qty_vs_batch_qty/stock_qty_vs_batch_qty.py
@@ -44,7 +44,12 @@ def get_data(filters=None):
 	item = filters.get("item")
 	batch_no = filters.get("batch")
 
-	batch_sle_data = get_batch_qty(item_code=item, batch_no=batch_no) or []
+	batch_sle_data = (
+		get_batch_qty(
+			item_code=item, batch_no=batch_no, for_stock_levels=True, consider_negative_batches=True
+		)
+		or []
+	)
 
 	stock_qty_map = {}
 	for row in batch_sle_data:
@@ -69,17 +74,17 @@ def get_data(filters=None):
 	batch_records = query.run(as_dict=True) or []
 
 	result = []
-	for batch_doc in batch_records:
-		name = batch_doc.get("name")
-		batch_qty = batch_doc.get("batch_qty") or 0
+	for row in batch_records:
+		name = row.get("name")
+		batch_qty = row.get("batch_qty") or 0
 		stock_qty = stock_qty_map.get(name, 0)
 		difference = stock_qty - batch_qty
 
 		if difference != 0:
 			result.append(
 				{
-					"item_code": batch_doc.get("item"),
-					"item_name": batch_doc.get("item_name"),
+					"item_code": row.get("item"),
+					"item_name": row.get("item_name"),
 					"batch": name,
 					"batch_qty": batch_qty,
 					"stock_qty": stock_qty,
@@ -91,15 +96,25 @@ def get_data(filters=None):
 
 
 @frappe.whitelist()
-def update_batch_qty(batches=None):
-	if not batches:
+def update_batch_qty(selected_batches=None):
+	if not selected_batches:
 		return
 
-	batches = json.loads(batches)
-	for batch in batches:
-		batch_name = batch.get("batch")
-		stock_qty = batch.get("stock_qty")
+	selected_batches = json.loads(selected_batches)
+	for row in selected_batches:
+		batch_name = row.get("batch")
 
-		frappe.db.set_value("Batch", batch_name, "batch_qty", stock_qty)
+		batches = get_batch_qty(
+			batch_no=batch_name,
+			item_code=row.get("item_code"),
+			for_stock_levels=True,
+			consider_negative_batches=True,
+		)
+		batch_qty = 0.0
+		if batches:
+			for batch in batches:
+				batch_qty += batch.get("qty")
+
+		frappe.db.set_value("Batch", batch_name, "batch_qty", batch_qty)
 
 	frappe.msgprint(_("Batch Qty updated successfully"), alert=True)