diff --git a/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.js b/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.js
index f523cf21bd4..3980370370d 100644
--- a/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.js
+++ b/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.js
@@ -29,6 +29,29 @@ frappe.ui.form.on('Inpatient Medication Entry', {
 				}
 			};
 		});
+
+		if (frm.doc.__islocal || frm.doc.docstatus !== 0)
+			return;
+
+		frm.add_custom_button(__('Make Stock Entry'), function() {
+			frappe.call({
+				method: 'erpnext.healthcare.doctype.inpatient_medication_entry.inpatient_medication_entry.make_difference_stock_entry',
+				args: {	docname: frm.doc.name },
+				freeze: true,
+				callback: function(r) {
+					if (r.message) {
+						var doclist = frappe.model.sync(r.message);
+						frappe.set_route('Form', doclist[0].doctype, doclist[0].name);
+					} else {
+						frappe.msgprint({
+							title: __('No Drug Shortage'),
+							message: __('All the drugs are available with sufficient qty to process this Inpatient Medication Entry.'),
+							indicator: 'green'
+						});
+					}
+				}
+			})
+		});
 	},
 
 	patient: function(frm) {
diff --git a/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.py b/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.py
index 5dac23abd90..5a2a0e54aa5 100644
--- a/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.py
+++ b/erpnext/healthcare/doctype/inpatient_medication_entry/inpatient_medication_entry.py
@@ -142,25 +142,32 @@ class InpatientMedicationEntry(Document):
 		return orders, order_entry_map
 
 	def check_stock_qty(self):
-		from erpnext.stock.stock_ledger import NegativeStockError
+		drug_shortage = get_drug_shortage_map(self.medication_orders, self.warehouse)
 
-		drug_availability = dict()
-		for d in self.medication_orders:
-			if not drug_availability.get(d.drug_code):
-				drug_availability[d.drug_code] = 0
-			drug_availability[d.drug_code] += flt(d.dosage)
+		if drug_shortage:
+			message = _('Quantity not available for the following items in warehouse {0}. ').format(frappe.bold(self.warehouse))
+			message += _('Please enable Allow Negative Stock in Stock Settings or create Stock Entry to proceed.')
 
-		for drug, dosage in drug_availability.items():
-			available_qty = get_latest_stock_qty(drug, self.warehouse)
+			formatted_item_rows = ''
 
-			# validate qty
-			if flt(available_qty) < flt(dosage):
-				frappe.throw(_('Quantity not available for {0} in warehouse {1}').format(
-					frappe.bold(drug), frappe.bold(self.warehouse))
-					+ '<br><br>' + _('Available quantity is {0}, you need {1}').format(
-					frappe.bold(available_qty), frappe.bold(dosage))
-					+ '<br><br>' + _('Please enable Allow Negative Stock in Stock Settings or create Stock Entry to proceed.'),
-					NegativeStockError, title=_('Insufficient Stock'))
+			for drug, shortage_qty in drug_shortage.items():
+				item_link = get_link_to_form('Item', drug)
+				formatted_item_rows += """
+					<td>{0}</td>
+					<td>{1}</td>
+				</tr>""".format(item_link, frappe.bold(shortage_qty))
+
+			message += """
+				<table class='table'>
+					<thead>
+						<th>{0}</th>
+						<th>{1}</th>
+					</thead>
+					{2}
+				</table>
+			""".format(_('Drug Code'), _('Shortage Qty'), formatted_item_rows)
+
+			frappe.throw(message, title=_('Insufficient Stock'), is_minimizable=True, wide=True)
 
 	def make_stock_entry(self):
 		stock_entry = frappe.new_doc('Stock Entry')
@@ -276,4 +283,55 @@ def get_current_healthcare_service_unit(inpatient_record):
 	ip_record = frappe.get_doc('Inpatient Record', inpatient_record)
 	if ip_record.inpatient_occupancies:
 		return ip_record.inpatient_occupancies[-1].service_unit
-	return
\ No newline at end of file
+	return
+
+
+def get_drug_shortage_map(medication_orders, warehouse):
+	"""
+		Returns a dict like { drug_code: shortage_qty }
+	"""
+	drug_requirement = dict()
+	for d in medication_orders:
+		if not drug_requirement.get(d.drug_code):
+			drug_requirement[d.drug_code] = 0
+		drug_requirement[d.drug_code] += flt(d.dosage)
+
+	drug_shortage = dict()
+	for drug, required_qty in drug_requirement.items():
+		available_qty = get_latest_stock_qty(drug, warehouse)
+		if flt(required_qty) > flt(available_qty):
+			drug_shortage[drug] = flt(flt(required_qty) - flt(available_qty))
+
+	return drug_shortage
+
+
+@frappe.whitelist()
+def make_difference_stock_entry(docname):
+	doc = frappe.get_doc('Inpatient Medication Entry', docname)
+	drug_shortage = get_drug_shortage_map(doc.medication_orders, doc.warehouse)
+
+	if not drug_shortage:
+		return None
+
+	stock_entry = frappe.new_doc('Stock Entry')
+	stock_entry.purpose = 'Material Transfer'
+	stock_entry.set_stock_entry_type()
+	stock_entry.to_warehouse = doc.warehouse
+	stock_entry.company = doc.company
+	cost_center = frappe.get_cached_value('Company',  doc.company,  'cost_center')
+	expense_account = get_account(None, 'expense_account', 'Healthcare Settings', doc.company)
+
+	for drug, shortage_qty in drug_shortage.items():
+		se_child = stock_entry.append('items')
+		se_child.item_code = drug
+		se_child.item_name = frappe.db.get_value('Item', drug, 'stock_uom')
+		se_child.uom = frappe.db.get_value('Item', drug, 'stock_uom')
+		se_child.stock_uom = se_child.uom
+		se_child.qty = flt(shortage_qty)
+		se_child.t_warehouse = doc.warehouse
+		# in stock uom
+		se_child.conversion_factor = 1
+		se_child.cost_center = cost_center
+		se_child.expense_account = expense_account
+
+	return stock_entry