diff --git a/core/src/main/java/io/substrait/relation/Set.java b/core/src/main/java/io/substrait/relation/Set.java
index 6160c2460..4efef01e2 100644
--- a/core/src/main/java/io/substrait/relation/Set.java
+++ b/core/src/main/java/io/substrait/relation/Set.java
@@ -11,9 +11,11 @@ public abstract class Set extends AbstractRel implements HasExtension {
   public static enum SetOp {
     UNKNOWN(SetRel.SetOp.SET_OP_UNSPECIFIED),
     MINUS_PRIMARY(SetRel.SetOp.SET_OP_MINUS_PRIMARY),
+    MINUS_PRIMARY_ALL(SetRel.SetOp.SET_OP_MINUS_PRIMARY_ALL),
     MINUS_MULTISET(SetRel.SetOp.SET_OP_MINUS_MULTISET),
     INTERSECTION_PRIMARY(SetRel.SetOp.SET_OP_INTERSECTION_PRIMARY),
     INTERSECTION_MULTISET(SetRel.SetOp.SET_OP_INTERSECTION_MULTISET),
+    INTERSECTION_MULTISET_ALL(SetRel.SetOp.SET_OP_INTERSECTION_MULTISET_ALL),
     UNION_DISTINCT(SetRel.SetOp.SET_OP_UNION_DISTINCT),
     UNION_ALL(SetRel.SetOp.SET_OP_UNION_ALL);
 
diff --git a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
index 8691466c6..3cdbfd3d1 100644
--- a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
+++ b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelNodeConverter.java
@@ -211,12 +211,17 @@ public RelNode visit(Set set) throws RuntimeException {
             input -> {
               relBuilder.push(input.accept(this));
             });
+    // TODO: MINUS_MULTISET and INTERSECTION_PRIMARY mappings are set to be removed as they do not
+    //   correspond to the Calcite relations they are associated with. They are retained for now
+    //   to enable users to migrate off of them.
+    //   See:  https://github.com/substrait-io/substrait-java/issues/303
     var builder =
         switch (set.getSetOp()) {
           case MINUS_PRIMARY -> relBuilder.minus(false, numInputs);
-          case MINUS_MULTISET -> relBuilder.minus(true, numInputs);
-          case INTERSECTION_PRIMARY -> relBuilder.intersect(false, numInputs);
-          case INTERSECTION_MULTISET -> relBuilder.intersect(true, numInputs);
+          case MINUS_PRIMARY_ALL, MINUS_MULTISET -> relBuilder.minus(true, numInputs);
+          case INTERSECTION_PRIMARY, INTERSECTION_MULTISET -> relBuilder.intersect(
+              false, numInputs);
+          case INTERSECTION_MULTISET_ALL -> relBuilder.intersect(true, numInputs);
           case UNION_DISTINCT -> relBuilder.union(false, numInputs);
           case UNION_ALL -> relBuilder.union(true, numInputs);
           case UNKNOWN -> throw new UnsupportedOperationException(
diff --git a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelVisitor.java b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelVisitor.java
index cd10a7ef3..a367e0217 100644
--- a/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelVisitor.java
+++ b/isthmus/src/main/java/io/substrait/isthmus/SubstraitRelVisitor.java
@@ -217,14 +217,15 @@ public Rel visit(org.apache.calcite.rel.core.Union union) {
   @Override
   public Rel visit(org.apache.calcite.rel.core.Intersect intersect) {
     var inputs = apply(intersect.getInputs());
-    var setOp = intersect.all ? Set.SetOp.INTERSECTION_MULTISET : Set.SetOp.INTERSECTION_PRIMARY;
+    var setOp =
+        intersect.all ? Set.SetOp.INTERSECTION_MULTISET_ALL : Set.SetOp.INTERSECTION_MULTISET;
     return Set.builder().inputs(inputs).setOp(setOp).build();
   }
 
   @Override
   public Rel visit(org.apache.calcite.rel.core.Minus minus) {
     var inputs = apply(minus.getInputs());
-    var setOp = minus.all ? Set.SetOp.MINUS_MULTISET : Set.SetOp.MINUS_PRIMARY;
+    var setOp = minus.all ? Set.SetOp.MINUS_PRIMARY_ALL : Set.SetOp.MINUS_PRIMARY;
     return Set.builder().inputs(inputs).setOp(setOp).build();
   }
 
diff --git a/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java b/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
index b7cc0d141..deac90e87 100644
--- a/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
+++ b/isthmus/src/test/java/io/substrait/isthmus/utils/SetUtils.java
@@ -21,12 +21,12 @@ public static String getSetQuery(Set.SetOp op, boolean multi) {
     String opString =
         switch (op) {
           case MINUS_PRIMARY -> "EXCEPT";
-          case MINUS_MULTISET -> "EXCEPT ALL";
-          case INTERSECTION_PRIMARY -> "INTERSECT";
-          case INTERSECTION_MULTISET -> "INTERSECT ALL";
+          case MINUS_PRIMARY_ALL -> "EXCEPT ALL";
+          case INTERSECTION_MULTISET -> "INTERSECT";
+          case INTERSECTION_MULTISET_ALL -> "INTERSECT ALL";
           case UNION_DISTINCT -> "UNION";
           case UNION_ALL -> "UNION ALL";
-          case UNKNOWN -> throw new UnsupportedOperationException(
+          default -> throw new UnsupportedOperationException(
               "Unknown set operation is not supported");
         };
 
@@ -49,10 +49,16 @@ public static String getSetQuery(Set.SetOp op, boolean multi) {
     }
   }
 
-  // Generate all combinations excluding the UNKNOWN operator
+  // Generate all SetOp types excluding:
+  // * MINUS_MULTISET, INTERSECTION_PRIMARY: do not map to Calcite relations
+  // * UNKNOWN: invalid
   public static Stream<Arguments> setTestConfig() {
     return Arrays.stream(Set.SetOp.values())
-        .filter(op -> op != Set.SetOp.UNKNOWN)
+        .filter(
+            op ->
+                op != Set.SetOp.UNKNOWN
+                    && op != Set.SetOp.MINUS_MULTISET
+                    && op != Set.SetOp.INTERSECTION_PRIMARY)
         .flatMap(op -> Stream.of(arguments(op, false), arguments(op, true)));
   }
 }
diff --git a/substrait b/substrait
index bc4d6fb9b..297715c7b 160000
--- a/substrait
+++ b/substrait
@@ -1 +1 @@
-Subproject commit bc4d6fb9bc0435c3db24172566c343e119fc50a9
+Subproject commit 297715c7b7b6cb367973cc64c1a2a296df12a812