diff --git a/Source/cmExportFileGenerator.cxx b/Source/cmExportFileGenerator.cxx
index 42fce6d40..25ffe1a0c 100644
--- a/Source/cmExportFileGenerator.cxx
+++ b/Source/cmExportFileGenerator.cxx
@@ -277,6 +277,8 @@ static bool checkInterfaceDirs(const std::string &prepro,
            "  \"" << *li << "\"";
       target->GetMakefile()->IssueMessage(messageType, e.str());
       }
+    bool inBinary = isSubDirectory(li->c_str(), topBinaryDir);
+    bool inSource = isSubDirectory(li->c_str(), topSourceDir);
     if (isSubDirectory(li->c_str(), installDir))
       {
       // The include directory is inside the install tree.  If the
@@ -284,8 +286,8 @@ static bool checkInterfaceDirs(const std::string &prepro,
       // fall through to the checks below that the include directory is not
       // also inside the source tree or build tree.
       bool shouldContinue =
-          isSubDirectory(installDir, topBinaryDir)
-        || isSubDirectory(installDir, topSourceDir);
+        (!inBinary || isSubDirectory(installDir, topBinaryDir)) &&
+        (!inSource || isSubDirectory(installDir, topSourceDir));
 
       if (!shouldContinue)
         {
@@ -317,7 +319,7 @@ static bool checkInterfaceDirs(const std::string &prepro,
         continue;
         }
       }
-    if (isSubDirectory(li->c_str(), topBinaryDir))
+    if (inBinary)
       {
       e << "Target \"" << target->GetName() << "\" "
            "INTERFACE_INCLUDE_DIRECTORIES property contains path:\n"
@@ -326,7 +328,7 @@ static bool checkInterfaceDirs(const std::string &prepro,
       }
     if (!inSourceBuild)
       {
-      if (isSubDirectory(li->c_str(), topSourceDir))
+      if (inSource)
         {
         e << "Target \"" << target->GetName() << "\" "
             "INTERFACE_INCLUDE_DIRECTORIES property contains path:\n"