diff --git a/CHANGES.md b/CHANGES.md
index 8b3e4411a..e1bcdafa1 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -5,6 +5,7 @@
 ### Features
 
 * mask: Add `--mask-gaps` option to `augur mask` to allow masking of gaps at terminals via `--mask-gaps terminals` or all gaps via `--mask-gaps all`. [#1286][] (@corneliusroemer)
+* mask: Warn on empty mask file instead of error. Introduced to allow empty stub files when setting up builds and to prevent necessary workflow changes when all mask sites are removed. [#1287][] (@corneliusroemer)
 
 ### Bug fixes
 
@@ -12,6 +13,7 @@
 
 [#1285]: https://github.com/nextstrain/augur/pull/1285
 [#1286]: https://github.com/nextstrain/augur/pull/1286
+[#1287]: https://github.com/nextstrain/augur/pull/1286
 
 ## 22.3.0 (14 August 2023)
 
diff --git a/augur/mask.py b/augur/mask.py
index e3c26bc80..20e7c712e 100644
--- a/augur/mask.py
+++ b/augur/mask.py
@@ -231,8 +231,7 @@ def run(args):
             print("ERROR: File {} does not exist!".format(args.mask_file))
             sys.exit(1)
         if os.path.getsize(args.mask_file) == 0:
-            print("ERROR: {} is an empty file.".format(args.mask_file))
-            sys.exit(1)
+            print(f"WARN: The mask file {args.mask_file} is an empty file.")
     if not any((args.mask_file, args.mask_gaps, args.mask_from_beginning, args.mask_from_end, args.mask_sites, args.mask_invalid)):
         print("No masking sites provided. Must include one of --mask, --mask-gaps, --mask-from-beginning, --mask-from-end, --mask-invalid, or --mask-sites")
         sys.exit(1)