diff --git a/metomi/rose/checksum.py b/metomi/rose/checksum.py
index c8dfe360f2..d8fbb1db95 100644
--- a/metomi/rose/checksum.py
+++ b/metomi/rose/checksum.py
@@ -70,8 +70,16 @@ def get_checksum(name, checksum_func=None):
             for filename in filenames:
                 filepath = os.path.join(path, filename)
                 source = os.path.join(name, filepath)
-                checksum = checksum_func(source, name)
-                mode = os.stat(os.path.realpath(source)).st_mode
+
+                if os.path.islink(source) and not os.path.exists(source):
+                    # If the source is a broken link within a directory
+                    # install without failing (unlike a single file)
+                    checksum = os.path.realpath(source)
+                    mode = os.lstat(source).st_mode
+                else:
+                    checksum = checksum_func(source, name)
+                    mode = os.stat(os.path.realpath(source)).st_mode
+
                 path_and_checksum_list.append((filepath, checksum, mode))
     return path_and_checksum_list
 
diff --git a/metomi/rose/loc_handlers/rsync_remote_check.py b/metomi/rose/loc_handlers/rsync_remote_check.py
index 0e7c2928d6..69fa9eb141 100644
--- a/metomi/rose/loc_handlers/rsync_remote_check.py
+++ b/metomi/rose/loc_handlers/rsync_remote_check.py
@@ -62,7 +62,10 @@ def main(path, str_blob, str_tree):
                 if filename.startswith("."):
                     continue
                 name = os.path.join(dirpath, filename)
-                stat = os.stat(name)
+                if os.path.islink(name) and not os.path.exists(name):
+                    stat = os.lstat(name)
+                else:
+                    stat = os.stat(name)
                 print(stat.st_mode, stat.st_mtime, stat.st_size, name)
     elif os.path.isfile(path):
         print(str_blob)
diff --git a/metomi/rose/tests/test_checksum.py b/metomi/rose/tests/test_checksum.py
new file mode 100644
index 0000000000..0da148b93b
--- /dev/null
+++ b/metomi/rose/tests/test_checksum.py
@@ -0,0 +1,82 @@
+# Copyright (C) British Crown (Met Office) & Contributors.
+# This file is part of Rose, a framework for meteorological suites.
+#
+# Rose is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Rose is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Rose. If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------
+
+import hashlib
+from pathlib import Path
+import pytest
+
+from metomi.rose.checksum import get_checksum
+
+HELLO_WORLD = hashlib.md5(b'Hello World').hexdigest()
+HELLO_JUPITER = hashlib.md5(b'Hello Jupiter').hexdigest()
+
+
+@pytest.fixture(scope='module')
+def checksums_setup(tmp_path_factory):
+    """provide some exemplars for checksum to work on."""
+    tmp_path = tmp_path_factory.getbasetemp()
+    (tmp_path / 'foo').write_text('Hello World')
+    (tmp_path / 'bar').mkdir()
+    (tmp_path / 'bar/baz').write_text('Hello Jupiter')
+    (tmp_path / 'goodlink').symlink_to('foo')
+    (tmp_path / 'badlink').symlink_to('bad')
+    yield tmp_path
+
+
+@pytest.fixture(scope='module')
+def checksums_dir(checksums_setup):
+    yield (
+        {a: (b, c) for a, b, c in get_checksum(str(checksums_setup))},
+        checksums_setup
+    )
+
+
+def test_checksum_single_file(checksums_setup):
+    res = get_checksum(str(checksums_setup / 'foo'))[0][1]
+    assert res == HELLO_WORLD
+
+
+def test_checksum_custom_checksum_function(checksums_setup):
+    res = get_checksum(
+        str(checksums_setup / 'foo'),
+        # Last 3 letters of the reversed filename:
+        checksum_func=lambda x, _: x[-1:-4:-1]
+    )[0][1]
+    assert res == 'oof'
+
+
+def test_get_checksum_for_all_files(checksums_dir):
+    assert len(checksums_dir[0]) == 7
+
+
+def test_get_checksum_for_goodlink(checksums_dir):
+    assert checksums_dir[0]['goodlink'][0] == HELLO_WORLD
+
+
+def test_get_checksum_for_badlink(checksums_dir):
+    assert checksums_dir[0]['badlink'][0] == str(checksums_dir[1] / 'bad')
+
+
+def test_get_checksum_for_subdir_file(checksums_dir):
+    assert checksums_dir[0]['bar/baz'][0] == HELLO_JUPITER
+
+
+def test_get_checksum_for_non_path():
+    unlikely = '/var/tmp/ariuaibvnoijunhoiujoiuj'
+    assert not Path(unlikely).exists()
+    with pytest.raises(FileNotFoundError, match=unlikely):
+        get_checksum(unlikely)
diff --git a/sphinx/api/configuration/file-creation.rst b/sphinx/api/configuration/file-creation.rst
index afef6ac372..8ce23e4e4f 100644
--- a/sphinx/api/configuration/file-creation.rst
+++ b/sphinx/api/configuration/file-creation.rst
@@ -116,6 +116,11 @@ root directory to install file targets with a relative path:
          ``~/.ssh/config`` to specify the user ID for logging into ``HOST``
          if required.
 
+      .. note::
+
+         * When installing files, broken symbolic links are rejected.
+         * When installing directories containing broken symlinks
+           they will be copied.
 
    .. rose:conf:: file:TARGET
 
diff --git a/t/rose-app-run/29-dir-symlink-no-source.t b/t/rose-app-run/29-dir-symlink-no-source.t
new file mode 100644
index 0000000000..a19434a65a
--- /dev/null
+++ b/t/rose-app-run/29-dir-symlink-no-source.t
@@ -0,0 +1,60 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------------------------
+# Copyright (C) British Crown (Met Office) & Contributors.
+#
+# This file is part of Rose, a framework for meteorological suites.
+#
+# Rose is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# Rose is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with Rose. If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+# Test "rose app-run", file installation will not fail if a broken
+# symlink is contained in a repository or directory.
+# See https://github.com/metomi/rose/issues/2946
+
+. "$(dirname "$0")/test_header"
+
+tests 4
+
+test_init <<__CONFIG__
+[command]
+default=true
+
+[file:destination]
+source=${TEST_DIR}/source
+__CONFIG__
+
+# Create a broken symlink dir
+mkdir -p ${TEST_DIR}/source/
+touch ${TEST_DIR}/source/missing
+ln -s ${TEST_DIR}/source/missing ${TEST_DIR}/source/link
+rm ${TEST_DIR}/source/missing
+
+test_setup
+
+# It doesn't fail when rsync installs broken symlink dirs:
+run_pass "${TEST_KEY_BASE}-rsync" rose app-run --config=../config
+file_grep_fail "${TEST_KEY_BASE}-rsync.err" \
+    "No such file" \
+    "${TEST_KEY_BASE}-rsync.err"
+
+# Turn the source file into a Git repo and try to use the git file-handler:
+git -C ${TEST_DIR}/source init
+git -C ${TEST_DIR}/source add .
+git -C ${TEST_DIR}/source commit -a -m "my_commit"
+sed -i 'sXsource=.*Xsource=git:../source::./::HEADX' ../config/rose-app.conf
+
+# It doesn't fail when git installs broken symlink dirs:
+run_pass "${TEST_KEY_BASE}-git" rose app-run --config=../config
+file_grep_fail "${TEST_KEY_BASE}-git.err" \
+    "No such file" \
+    "${TEST_KEY_BASE}-git.err"