diff --git a/qiskit/transpiler/passes/utils/check_map.py b/qiskit/transpiler/passes/utils/check_map.py
index f71e5640f16..d56a709253c 100644
--- a/qiskit/transpiler/passes/utils/check_map.py
+++ b/qiskit/transpiler/passes/utils/check_map.py
@@ -15,6 +15,7 @@
 from qiskit.transpiler.basepasses import AnalysisPass
 from qiskit.transpiler.target import Target
 from qiskit.circuit.controlflow import ControlFlowOp
+from qiskit.converters import circuit_to_dag
 
 
 class CheckMap(AnalysisPass):
@@ -64,35 +65,30 @@ def run(self, dag):
         Args:
             dag (DAGCircuit): DAG to map.
         """
-        from qiskit.converters import circuit_to_dag
-
-        self.property_set[self.property_set_field] = True
-
         if not self.qargs:
+            self.property_set[self.property_set_field] = True
             return
+        wire_map = {bit: index for index, bit in enumerate(dag.qubits)}
+        self.property_set[self.property_set_field] = self._recurse(dag, wire_map)
 
-        qubit_indices = {bit: index for index, bit in enumerate(dag.qubits)}
+    def _recurse(self, dag, wire_map) -> bool:
         for node in dag.op_nodes(include_directives=False):
-            is_controlflow_op = isinstance(node.op, ControlFlowOp)
-            if len(node.qargs) == 2 and not is_controlflow_op:
-                if dag.has_calibration_for(node):
-                    continue
-                physical_q0 = qubit_indices[node.qargs[0]]
-                physical_q1 = qubit_indices[node.qargs[1]]
-                if (physical_q0, physical_q1) not in self.qargs:
-                    self.property_set["check_map_msg"] = "{}({}, {}) failed".format(
-                        node.name,
-                        physical_q0,
-                        physical_q1,
-                    )
-                    self.property_set[self.property_set_field] = False
-                    return
-            elif is_controlflow_op:
-                order = [qubit_indices[bit] for bit in node.qargs]
+            if isinstance(node.op, ControlFlowOp):
                 for block in node.op.blocks:
-                    dag_block = circuit_to_dag(block)
-                    mapped_dag = dag.copy_empty_like()
-                    mapped_dag.compose(dag_block, qubits=order)
-                    self.run(mapped_dag)
-                    if not self.property_set[self.property_set_field]:
-                        return
+                    inner_wire_map = {
+                        inner: wire_map[outer] for inner, outer in zip(block.qubits, node.qargs)
+                    }
+                    if not self._recurse(circuit_to_dag(block), inner_wire_map):
+                        return False
+            elif (
+                len(node.qargs) == 2
+                and not dag.has_calibration_for(node)
+                and (wire_map[node.qargs[0]], wire_map[node.qargs[1]]) not in self.qargs
+            ):
+                self.property_set["check_map_msg"] = "{}({}, {}) failed".format(
+                    node.name,
+                    wire_map[node.qargs[0]],
+                    wire_map[node.qargs[1]],
+                )
+                return False
+        return True
diff --git a/releasenotes/notes/fix-checkmap-nested-condition-1776f952f6c6722a.yaml b/releasenotes/notes/fix-checkmap-nested-condition-1776f952f6c6722a.yaml
new file mode 100644
index 00000000000..0805524cd7b
--- /dev/null
+++ b/releasenotes/notes/fix-checkmap-nested-condition-1776f952f6c6722a.yaml
@@ -0,0 +1,6 @@
+---
+fixes:
+  - |
+    The :class:`.CheckMap` transpiler pass will no longer spuriously error when dealing with nested
+    conditional structures created by the control-flow builder interface.  See `#10394
+    <https://github.com/Qiskit/qiskit-terra/issues/10394>`__.
diff --git a/test/python/transpiler/test_check_map.py b/test/python/transpiler/test_check_map.py
index 8368e3cc94e..27802c708a9 100644
--- a/test/python/transpiler/test_check_map.py
+++ b/test/python/transpiler/test_check_map.py
@@ -255,6 +255,28 @@ def test_nested_controlflow_false(self):
         pass_.run(dag)
         self.assertFalse(pass_.property_set["is_swap_mapped"])
 
+    def test_nested_conditional_unusual_bit_order(self):
+        """Test that `CheckMap` succeeds when inner conditional blocks have clbits that are involved
+        in their own (nested conditionals), and the binding order is not the same as the
+        bit-definition order.  See gh-10394."""
+        qr = QuantumRegister(2, "q")
+        cr1 = ClassicalRegister(2, "c1")
+        cr2 = ClassicalRegister(2, "c2")
+
+        # Note that the bits here are not in the same order as in the outer circuit object, but they
+        # are the same as the binding order in the `if_test`, so everything maps `{x: x}` and it
+        # should all be fine.  This kind of thing is a staple of the control-flow builders.
+        inner_order = [cr2[0], cr1[0], cr2[1], cr1[1]]
+        inner = QuantumCircuit(qr, inner_order, cr1, cr2)
+        inner.cx(0, 1).c_if(cr2, 3)
+
+        outer = QuantumCircuit(qr, cr1, cr2)
+        outer.if_test((cr1, 3), inner, outer.qubits, inner_order)
+
+        pass_ = CheckMap(CouplingMap.from_line(2))
+        pass_(outer)
+        self.assertTrue(pass_.property_set["is_swap_mapped"])
+
 
 if __name__ == "__main__":
     unittest.main()