Index: src/wp-admin/includes/theme.php
===================================================================
--- src/wp-admin/includes/theme.php	(revision 38779)
+++ src/wp-admin/includes/theme.php	(working copy)
@@ -544,6 +544,14 @@
 		$slug = $theme->get_stylesheet();
 		$encoded_slug = urlencode( $slug );
 
+		if ( isset( $updates[ $slug ] ) ) {
+			$hasUpdate = true;
+			$hasPackage = ! empty( $updates[ $slug ][ 'package' ] ) ? true : false;
+		} else {
+			$hasUpdate = false;
+			$hasPackage = false;
+		}
+
 		$parent = false;
 		if ( $theme->parent() ) {
 			$parent = $theme->parent()->display( 'Name' );
@@ -571,7 +579,8 @@
 			'tags'         => $theme->display( 'Tags' ),
 			'parent'       => $parent,
 			'active'       => $slug === $current_theme,
-			'hasUpdate'    => isset( $updates[ $slug ] ),
+			'hasUpdate'    => $hasUpdate,
+			'hasPackage'   => $hasPackage,
 			'update'       => get_theme_update_available( $theme ),
 			'actions'      => array(
 				'activate' => current_user_can( 'switch_themes' ) ? wp_nonce_url( admin_url( 'themes.php?action=activate&stylesheet=' . $encoded_slug ), 'switch-theme_' . $slug ) : null,
Index: src/wp-admin/themes.php
===================================================================
--- src/wp-admin/themes.php	(revision 38779)
+++ src/wp-admin/themes.php	(working copy)
@@ -377,7 +377,7 @@
 		<div class="theme-screenshot blank"></div>
 	<# } #>
 
-	<# if ( data.hasUpdate ) { #>
+	<# if ( data.hasUpdate && data.hasPackage ) { #>
 		<div class="update-message notice inline notice-warning notice-alt"><p><?php _e( 'New version available. <button class="button-link" type="button">Update now</button>' ); ?></p></div>
 	<# } #>