diff --git a/master_changes.md b/master_changes.md
index 1ab70ae3e4a..3cf01ec9701 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -59,6 +59,7 @@ users)
 ## Opamfile
 
 ## External dependencies
+ * Correct flags passed to Cygwin setup for external installations [#6045 @dra27 fixes #6041]
 
 ## Format upgrade
 
diff --git a/src/state/opamSysInteract.ml b/src/state/opamSysInteract.ml
index 5f649ffe271..4327dd736f7 100644
--- a/src/state/opamSysInteract.ml
+++ b/src/state/opamSysInteract.ml
@@ -1039,9 +1039,7 @@ let install_packages_commands_t ?(env=OpamVariable.Map.empty) config sys_package
      ] @ (if Cygwin.is_internal config then
             let common =
               [ "--upgrade-also";
-                "--only-site";
                 "--no-write-registry";
-                "--site"; Cygwin.mirror;
                 "--local-package-dir";
                 OpamFilename.Dir.to_string (Cygwin.internal_cygcache ());
               ]
@@ -1050,7 +1048,10 @@ let install_packages_commands_t ?(env=OpamVariable.Map.empty) config sys_package
               "--symlink-type" :: "native" :: common
             else
               common
-          else [])
+          else []) @ (if Cygwin.is_internal config || unsafe_yes then
+            [ "--only-site";
+              "--site"; Cygwin.mirror;
+            ])
     ],
     None
   | Debian ->