diff --git a/src/haddock/gear/clean_steps.py b/src/haddock/gear/clean_steps.py
index a73915d6f..933412d49 100644
--- a/src/haddock/gear/clean_steps.py
+++ b/src/haddock/gear/clean_steps.py
@@ -163,8 +163,8 @@ def unpack_compressed_and_archived_files(folders: Iterable[FilePathT],
                     pass
 
         for tar_file in tar_files:
-            with tarfile.open(tar_file) as fin:
-                fin.extractall(folder)
+            from haddock.libs.libio import extract_files_flat
+            extract_files_flat(tar_file, folder)
 
             tar_file.unlink()
 
diff --git a/src/haddock/gear/prepare_run.py b/src/haddock/gear/prepare_run.py
index 65b03cbb8..8f1ee274b 100644
--- a/src/haddock/gear/prepare_run.py
+++ b/src/haddock/gear/prepare_run.py
@@ -70,7 +70,7 @@
     )
 from haddock.gear.zerofill import zero_fill
 from haddock.libs.libfunc import not_none
-from haddock.libs.libio import make_writeable_recursive
+from haddock.libs.libio import make_writeable_recursive, extract_files_flat
 from haddock.libs.libutil import (
     extract_keys_recursive,
     recursive_convert_paths_to_strings,
@@ -1040,8 +1040,7 @@ def copy_input_files_to_data_dir(
                     # account for input .tgz files
                     if name.endswith("tgz"):
                         log.info(f"Uncompressing tar {value}")
-                        with tarfile.open(target_path) as fin:
-                            fin.extractall(pf)
+                        extract_files_flat(value, pf)
 
 
 def check_run_dir_exists(run_dir: FilePath) -> None:
diff --git a/src/haddock/libs/libio.py b/src/haddock/libs/libio.py
index 05e317a27..8f0b17c77 100644
--- a/src/haddock/libs/libio.py
+++ b/src/haddock/libs/libio.py
@@ -21,6 +21,7 @@
     Iterable,
     Mapping,
     Optional,
+    Union,
     )
 from haddock.libs.libontology import PDBFile
 from haddock.libs.libutil import sort_numbered_paths
@@ -613,3 +614,25 @@ def make_writeable_recursive(path: FilePath) -> None:
 
         for file_ in (os.path.join(root, f) for f in files):
             os.chmod(file_, get_perm(file_) | stat.S_IWUSR)
+
+
+def extract_files_flat(tar_path: Union[str, FilePath],
+                       dest_path: Union[str, FilePath]) -> None:
+    """
+    Extract files from a tarball to a destination folder.
+    
+    Parameters
+    ----------
+    tar_path : str or Path
+        The path to the tarball file.
+
+    dest_path : str or Path
+        The path to the destination folder.
+    """
+    with tarfile.open(tar_path, "r:gz") as tar:
+        for member in tar.getmembers():
+            # Extract only files (skip directories)
+            if member.isfile():
+                # Modify the member name to remove the directory structure
+                member.name = os.path.basename(member.name)
+                tar.extract(member, dest_path)
diff --git a/tests/golden_data/ambig.tbl.tgz b/tests/golden_data/ambig.tbl.tgz
new file mode 100644
index 000000000..56f4ef82e
Binary files /dev/null and b/tests/golden_data/ambig.tbl.tgz differ
diff --git a/tests/test_libio.py b/tests/test_libio.py
index b917a1242..305ac1dc5 100644
--- a/tests/test_libio.py
+++ b/tests/test_libio.py
@@ -1,12 +1,14 @@
 """Test libio."""
 import tempfile
 from pathlib import Path
+import shutil
 
 import pytest
 
 from haddock.libs.libio import (
     clean_suffix,
     dot_suffix,
+    extract_files_flat,
     file_exists,
     folder_exists,
     read_from_yaml,
@@ -15,6 +17,7 @@
     )
 
 from . import emptycfg, haddock3_yaml_cfg_examples
+from . import golden_data
 
 
 @pytest.mark.parametrize(
@@ -133,3 +136,15 @@ def test_folder_exists_wrong(i):
 def test_folder_exists_wrong_othererror():
     with pytest.raises(TypeError):
         folder_exists("some_bad_path", exception=TypeError)
+
+
+def test_extract_files_flat(monkeypatch):
+    """Test extract_files_flat."""
+    with tempfile.TemporaryDirectory() as tempdir:
+        reference_archive = Path(golden_data, "ambig.tbl.tgz")
+        shutil.copy(reference_archive, tempdir)
+        monkeypatch.chdir(tempdir)
+        archive = Path(reference_archive.name)
+        # extract the archive
+        extract_files_flat(archive, ".")
+        assert Path("ambig_1.tbl").exists()