diff --git a/payu/branch.py b/payu/branch.py
index 09f7d845..dd0c51b6 100644
--- a/payu/branch.py
+++ b/payu/branch.py
@@ -13,7 +13,7 @@
 from typing import Optional
 import shutil
 
-from ruamel.yaml import YAML, CommentedMap
+from ruamel.yaml import YAML, CommentedMap, constructor
 import git
 
 from payu.fsops import read_config, DEFAULT_CONFIG_FNAME, list_archive_dirs
@@ -67,8 +67,18 @@ def add_restart_to_config(restart_path: Path, config_path: Path) -> None:
     restart in archive"""
 
     # Default ruamel yaml preserves comments and multiline strings
-    yaml = YAML()
-    config = yaml.load(config_path)
+    try:
+        yaml = YAML()
+        config = yaml.load(config_path)
+    except constructor.DuplicateKeyError as e:
+        # PyYaml which is used to read config allows duplicate keys
+        # These will get removed when the configuration file is modified
+        warnings.warn(
+            "Removing any subsequent duplicate keys from config.yaml"
+        )
+        yaml = YAML()
+        yaml.allow_duplicate_keys = True
+        config = yaml.load(config_path)
 
     # Add in restart path
     config['restart'] = str(restart_path)
diff --git a/payu/cli.py b/payu/cli.py
index 0a6348a3..87afc4c9 100644
--- a/payu/cli.py
+++ b/payu/cli.py
@@ -15,6 +15,7 @@
 import shlex
 import subprocess
 import sys
+import warnings
 
 import payu
 import payu.envmod as envmod
@@ -23,10 +24,17 @@
 from payu.schedulers import index as scheduler_index
 import payu.subcommands
 
-
 # Default configuration
 DEFAULT_CONFIG = 'config.yaml'
 
+# Force warnings.warn() to omit the source code line in the message
+formatwarning_orig = warnings.formatwarning
+warnings.formatwarning = (
+    lambda message, category, filename, lineno, line=None: (
+        formatwarning_orig(message, category, filename, lineno, line='')
+    )
+)
+
 
 def parse():
     """Parse the command line inputs and execute the subcommand."""
diff --git a/payu/fsops.py b/payu/fsops.py
index ac91d82c..6560eade 100644
--- a/payu/fsops.py
+++ b/payu/fsops.py
@@ -17,6 +17,7 @@
 import shlex
 import subprocess
 from typing import Union, List
+import warnings
 
 # Extensions
 import yaml
@@ -62,6 +63,27 @@ def movetree(src, dst, symlinks=False):
     shutil.rmtree(src)
 
 
+class DuplicateKeyWarnLoader(yaml.SafeLoader):
+    def construct_mapping(self, node, deep=False):
+        """Add warning for duplicate keys in yaml file, as currently
+        PyYAML overwrites duplicate keys even though in YAML, keys
+        are meant to be unique
+        """
+        mapping = {}
+        for key_node, value_node in node.value:
+            key = self.construct_object(key_node, deep=deep)
+            value = self.construct_object(value_node, deep=deep)
+            if key in mapping:
+                warnings.warn(
+                    "Duplicate key found in config.yaml: "
+                    f"key '{key}' with value '{value}'. "
+                    f"This overwrites the original value: '{mapping[key]}'"
+                )
+            mapping[key] = value
+
+        return super().construct_mapping(node, deep)
+
+
 def read_config(config_fname=None):
     """Parse input configuration file and return a config dict."""
 
@@ -70,7 +92,7 @@ def read_config(config_fname=None):
 
     try:
         with open(config_fname, 'r') as config_file:
-            config = yaml.safe_load(config_file)
+            config = yaml.load(config_file, Loader=DuplicateKeyWarnLoader)
 
         # NOTE: A YAML file with no content returns `None`
         if config is None:
diff --git a/test/test_payu.py b/test/test_payu.py
index cf180875..7ab218cf 100644
--- a/test/test_payu.py
+++ b/test/test_payu.py
@@ -1,6 +1,7 @@
 from io import StringIO
 import os
 from pathlib import Path
+import payu.branch
 import pytest
 import shutil
 import stat
@@ -432,3 +433,34 @@ def test_run_userscript_command(tmp_path):
 ])
 def test_needs_shell(command, expected):
     assert payu.fsops.needs_subprocess_shell(command) == expected
+
+
+def test_read_config_yaml_duplicate_key():
+    """The PyYAML library is used for reading config.yaml, but use ruamel yaml
+    is used in when modifying config.yaml as part of payu checkout
+    (ruamel is used to preserve comments and multi-line strings).
+    This led to bug #441, where pyyaml allowed duplicate keys but
+    ruamel.library raises an error
+    """
+    # Create a yaml file with a duplicate key
+    config_content = """
+pbs_flags: value1
+pbs_flags: value2
+"""
+    config_path = tmpdir / "config.yaml"
+    with config_path.open("w") as file:
+        file.write(config_content)
+
+    # Test read config passes without an error but a warning is raised
+    warn_msg = "Duplicate key found in config.yaml: key 'pbs_flags' with "
+    warn_msg += "value 'value2'. This overwrites the original value: 'value1'"
+    with pytest.warns(UserWarning, match=warn_msg):
+        payu.fsops.read_config(config_path)
+
+    restart_path = tmpdir / "restarts"
+
+    # Test add restart to config.yaml does not fail with an error, but
+    # still raises another warning that duplicates keys will be deleted
+    warn_msg = "Removing any subsequent duplicate keys from config.yaml"
+    with pytest.warns(UserWarning, match=warn_msg):
+        payu.branch.add_restart_to_config(restart_path, config_path)