diff --git a/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/ConfigUtils.java b/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/ConfigUtils.java
index 85e2dcab2742..f64355c5a5a6 100644
--- a/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/ConfigUtils.java
+++ b/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/ConfigUtils.java
@@ -77,15 +77,15 @@ public static Object getFiniteBalValue(String strValue, BFiniteType finiteType,
 
     public static boolean containsUnsupportedMembers(BUnionType unionType) {
         for (Type memberType : unionType.getMemberTypes()) {
-            if (!isSimpleSequenceType(TypeUtils.getImpliedType(memberType).getTag())) {
+            if (!isPrimitiveOrSequenceType(TypeUtils.getImpliedType(memberType).getTag())) {
                 return true;
             }
         }
         return false;
     }
 
-    private static boolean isSimpleSequenceType(int tag) {
-        return tag <= TypeTags.BOOLEAN_TAG || TypeTags.isXMLTypeTag(tag);
+    private static boolean isPrimitiveOrSequenceType(int tag) {
+        return tag == TypeTags.NULL_TAG || tag <= TypeTags.BOOLEAN_TAG || TypeTags.isXMLTypeTag(tag);
     }
 
     public static Object getUnionValue(VariableKey key, BUnionType unionType, String value, String arg) {
@@ -104,6 +104,8 @@ private static List<Object> getConvertibleMemberValues(String value, UnionType u
         List<Object> matchingValues = new ArrayList<>();
         for (Type type : unionType.getMemberTypes()) {
             switch (TypeUtils.getImpliedType(type).getTag()) {
+                case TypeTags.NULL_TAG:
+                    break;
                 case TypeTags.BYTE_TAG:
                     convertAndGetValuesFromString(matchingValues, TypeConverter::stringToByte, value);
                     break;
diff --git a/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/cli/CliProvider.java b/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/cli/CliProvider.java
index 182b01135066..003998ff95d3 100644
--- a/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/cli/CliProvider.java
+++ b/bvm/ballerina-runtime/src/main/java/io/ballerina/runtime/internal/configurable/providers/cli/CliProvider.java
@@ -220,12 +220,12 @@ public Optional<ConfigValue> getAsUnionAndMark(Module module, VariableKey key) {
         CliArg cliArg = getCliArg(module, key);
         BUnionType unionType = (BUnionType) ((BIntersectionType) key.type).getEffectiveType();
         boolean isEnum = SymbolFlags.isFlagOn(unionType.getFlags(), SymbolFlags.ENUM);
-        if (!isEnum && ConfigUtils.containsUnsupportedMembers(unionType)) {
-            throw new ConfigException(CONFIG_CLI_TYPE_NOT_SUPPORTED, key.variable, unionType);
-        }
         if (cliArg.value == null) {
             return Optional.empty();
         }
+        if (!isEnum && ConfigUtils.containsUnsupportedMembers(unionType)) {
+            throw new ConfigException(CONFIG_CLI_TYPE_NOT_SUPPORTED, key.variable, unionType);
+        }
         if (isEnum) {
             return getCliConfigValue(ConfigUtils.getFiniteValue(key, unionType, cliArg.value, cliArg.toString()));
         }
diff --git a/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/CliProviderTest.java b/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/CliProviderTest.java
index e8d3e2f1ca63..71a55055055e 100644
--- a/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/CliProviderTest.java
+++ b/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/CliProviderTest.java
@@ -211,6 +211,10 @@ public Object[][] unionDataProvider() {
                 PredefinedTypes.TYPE_DECIMAL), true);
         UnionType floatBoolen = TypeCreator.createUnionType(List.of(PredefinedTypes.TYPE_FLOAT,
                 PredefinedTypes.TYPE_BOOLEAN), true);
+        UnionType intNull = TypeCreator.createUnionType(List.of(PredefinedTypes.TYPE_INT,
+                PredefinedTypes.TYPE_NULL), true);
+        UnionType boolenNull = TypeCreator.createUnionType(List.of(PredefinedTypes.TYPE_BOOLEAN,
+                PredefinedTypes.TYPE_NULL), true);
         return new Object[][]{
                 {"stringInt", getIntersectionType(ROOT_MODULE, stringInt), strVal, "-CstringInt=test"},
                 {"intFloat", getIntersectionType(ROOT_MODULE, intFloat), 2.2d, "-CintFloat=2.2"},
@@ -218,6 +222,8 @@ public Object[][] unionDataProvider() {
                 {"intBoolean", getIntersectionType(ROOT_MODULE, intBoolean), 2L, "-CintBoolean=2"},
                 {"intDecimal", getIntersectionType(ROOT_MODULE, intDecimal), decimalVal, "-CintDecimal=3.23"},
                 {"floatBoolen", getIntersectionType(ROOT_MODULE, floatBoolen), true, "-CfloatBoolen=true"},
+                {"intNull", getIntersectionType(ROOT_MODULE, intNull), 87L, "-CintNull=87"},
+                {"boolenNull", getIntersectionType(ROOT_MODULE, boolenNull), true, "-CboolenNull=true"},
         };
     }
 
diff --git a/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/ConfigTest.java b/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/ConfigTest.java
index 16ecd652a26f..9807d9640e7e 100644
--- a/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/ConfigTest.java
+++ b/bvm/ballerina-runtime/src/test/java/io/ballerina/runtime/test/config/ConfigTest.java
@@ -258,4 +258,23 @@ public void testEnvVarUnsupportedErrors(String variableName, Type type, String e
         }
 
     }
+
+    @Test
+    public void testCliWhenUnsupportedTypesWithinToml() {
+        ArrayType arrayType = TypeCreator.createArrayType(TYPE_STRING);
+        VariableKey v1 = new VariableKey(module, "v1", PredefinedTypes.TYPE_INT, true);
+        Type v2Type = new BIntersectionType(module, new Type[]{arrayType, PredefinedTypes.TYPE_READONLY},
+                arrayType, 0, true);
+        VariableKey v2 = new VariableKey(module, "v2", v2Type, true);
+        RuntimeDiagnosticLog diagnosticLog = new RuntimeDiagnosticLog();
+        ConfigResolver configResolver =
+                new ConfigResolver(Map.ofEntries(Map.entry(module, new VariableKey[]{v1, v2})), diagnosticLog,
+                        List.of(new CliProvider(ROOT_MODULE, "-CmyOrg.test_module.v1=87"),
+                                new TomlFileProvider(ROOT_MODULE,
+                                        getConfigPath("UnsupportedCLITypeConfig.toml"), Set.of(module))));
+        Map<VariableKey, ConfigValue> configValueMap = configResolver.resolveConfigs();
+        Assert.assertEquals(configValueMap.get(v1).getValue(), 87L);
+        Assert.assertEquals(configValueMap.get(v2).getValue().toString(), "[\"hello\",\"world\"]");
+        Assert.assertEquals(0, diagnosticLog.getErrorCount());
+    }
 }
diff --git a/bvm/ballerina-runtime/src/test/resources/config_files/UnsupportedCLITypeConfig.toml b/bvm/ballerina-runtime/src/test/resources/config_files/UnsupportedCLITypeConfig.toml
new file mode 100644
index 000000000000..ed6a86aa838e
--- /dev/null
+++ b/bvm/ballerina-runtime/src/test/resources/config_files/UnsupportedCLITypeConfig.toml
@@ -0,0 +1,2 @@
+[myOrg.test_module]
+v2 = ["hello", "world"]