diff --git a/internal/zinc-core/src/main/scala/sbt/internal/inc/MappedVirtualFile.scala b/internal/zinc-core/src/main/scala/sbt/internal/inc/MappedVirtualFile.scala
index 4037971ab1..c124b46685 100644
--- a/internal/zinc-core/src/main/scala/sbt/internal/inc/MappedVirtualFile.scala
+++ b/internal/zinc-core/src/main/scala/sbt/internal/inc/MappedVirtualFile.scala
@@ -58,12 +58,15 @@ class MappedFileConverter(rootPaths: Map[String, Path], allowMachinePath: Boolea
       case Some((key, rootPath)) =>
         MappedVirtualFile(s"$${$key}/${rootPath.relativize(path)}".replace('\\', '/'), rootPaths)
       case _ =>
-        path match {
-          case p if p.toUri.getScheme == "jrt"         => DummyVirtualFile("rt.jar", p)
-          case p if p.getFileName.toString == "rt.jar" => DummyVirtualFile("rt.jar", p)
-          case p if allowMachinePath                   => MappedVirtualFile(s"$p".replace('\\', '/'), rootPaths)
-          case p                                       => sys.error(s"$p cannot be mapped using the root paths $rootPaths")
-        }
+        def isCtSym =
+          path.getFileSystem
+            .provider()
+            .getScheme == "jar" && path.getFileSystem.toString.endsWith("ct.sym")
+        def isJrt = path.getFileSystem.provider().getScheme == "jrt"
+        if (isJrt || path.getFileName.toString == "rt.jar" || isCtSym)
+          DummyVirtualFile("rt.jar", path)
+        else if (allowMachinePath) MappedVirtualFile(s"$path".replace('\\', '/'), rootPaths)
+        else sys.error(s"$path cannot be mapped using the root paths $rootPaths")
     }
   }
 }