diff --git a/CHANGELOG b/CHANGELOG
index cd7ec0ca5..ac2a6e686 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -12,6 +12,8 @@ NEXT
 - fix issue with detecting conftest files if the arguments contain
   "::" node id specifications (copy pasted from "-v" output)
 
+- fix issue544 by only removing "@NUM" at the end of "::" separated parts 
+  and if the part has an ".py" extension
 
 2.6
 -----------------------------------
diff --git a/_pytest/config.py b/_pytest/config.py
index 80a0c2c26..0b04ff1cc 100644
--- a/_pytest/config.py
+++ b/_pytest/config.py
@@ -863,9 +863,13 @@ def getcfg(args, inibasenames):
 
 
 def node_with_line_number(string):
-    split = string.split('[')
-    split[0] = re.sub(r'@\d+', '', split[0])
-    return '['.join(split)
+    newparts = []
+    for part in string.split("::"):
+        m = re.match(r'.*\.py@\d+$', part)
+        if m is not None:
+            part = part[:part.rfind("@")]
+        newparts.append(part)
+    return "::".join(newparts)
 
 
 def setns(obj, dic):
diff --git a/testing/test_parseopt.py b/testing/test_parseopt.py
index 2e19a90f4..360bbd13b 100644
--- a/testing/test_parseopt.py
+++ b/testing/test_parseopt.py
@@ -146,8 +146,17 @@ class TestParser:
         assert args.S == False
 
     def test_parse_removes_line_number_from_positional_arguments(self, parser):
-        args = parser.parse(['path@2::func', 'path2@5::func2[param with @]'])
-        assert getattr(args, parseopt.FILE_OR_DIR) == ['path::func', 'path2::func2[param with @]']
+        args = parser.parse(['path.txt@2::item',
+                             'path2.py::func2[param with .py@123]',
+                             'path.py@123',
+                             'hello/path.py@123',
+        ])
+        assert getattr(args, parseopt.FILE_OR_DIR) == [
+                    'path.txt@2::item',
+                    'path2.py::func2[param with .py@123]',
+                    'path.py',
+                    'hello/path.py',
+        ]
 
     def test_parse_defaultgetter(self):
         def defaultget(option):