diff --git a/sklearn/cross_validation.py b/sklearn/cross_validation.py
index 1da2121f85507..e9c1a70dd57d5 100644
--- a/sklearn/cross_validation.py
+++ b/sklearn/cross_validation.py
@@ -1772,7 +1772,7 @@ def _shuffle(y, labels, random_state):
         for label in np.unique(labels):
             this_mask = (labels == label)
             ind[this_mask] = random_state.permutation(ind[this_mask])
-    return y[ind]
+    return safe_indexing(y, ind)
 
 
 def check_cv(cv, X=None, y=None, classifier=False):
diff --git a/sklearn/model_selection/_validation.py b/sklearn/model_selection/_validation.py
index 88c3922f99363..0010b89c82778 100644
--- a/sklearn/model_selection/_validation.py
+++ b/sklearn/model_selection/_validation.py
@@ -636,7 +636,7 @@ def _shuffle(y, groups, random_state):
         for group in np.unique(groups):
             this_mask = (groups == group)
             indices[this_mask] = random_state.permutation(indices[this_mask])
-    return y[indices]
+    return safe_indexing(y, indices)
 
 
 def learning_curve(estimator, X, y, groups=None,