diff --git a/python-package/xgboost/sklearn.py b/python-package/xgboost/sklearn.py
index e1cde586543a..6f84f7a4a6f0 100644
--- a/python-package/xgboost/sklearn.py
+++ b/python-package/xgboost/sklearn.py
@@ -852,14 +852,18 @@ def fit(self, X, y, *, sample_weight=None, base_margin=None,
             self.classes_ = cp.unique(y.values)
             self.n_classes_ = len(self.classes_)
             can_use_label_encoder = False
-            if not cp.array_equal(self.classes_, cp.arange(self.n_classes_)):
+            expected_classes = cp.arange(self.n_classes_)
+            if (self.classes_.shape != expected_classes.shape or
+                    not (self.classes_ == expected_classes).all()):
                 raise ValueError(label_encoding_check_error)
         elif _is_cupy_array(y):
             import cupy as cp  # pylint: disable=E0401
             self.classes_ = cp.unique(y)
             self.n_classes_ = len(self.classes_)
             can_use_label_encoder = False
-            if not cp.array_equal(self.classes_, cp.arange(self.n_classes_)):
+            expected_classes = cp.arange(self.n_classes_)
+            if (self.classes_.shape != expected_classes.shape or
+                    not (self.classes_ == expected_classes).all()):
                 raise ValueError(label_encoding_check_error)
         else:
             self.classes_ = np.unique(y)