diff --git a/docs/api/changelog.rst b/docs/api/changelog.rst
index 0dd6c8165..a1bfc7b5e 100644
--- a/docs/api/changelog.rst
+++ b/docs/api/changelog.rst
@@ -69,6 +69,7 @@ Fixed
   :meth:`imod.mf6.Recharge.from_imod5_cap_data`,
   :meth:`imod.mf6.LayeredWell.from_imod5_cap_data` now regrids the iMOD5 CAP
   data to the MODFLOW6 target discretization.
+- Fixed confusing warning about inconsistent IPF columns when loading GEN files.
 
 Changed
 ~~~~~~~
diff --git a/imod/formats/common.py b/imod/formats/common.py
new file mode 100644
index 000000000..d2fbbdcf2
--- /dev/null
+++ b/imod/formats/common.py
@@ -0,0 +1,30 @@
+import csv
+
+
+def infer_delimwhitespace(line: str, ncol: int):
+    """
+    Infer whether the line is delimited by whitespace or commas, based on the
+    number of columns. Also returns whether the line has the amount of expected
+    columns if delimited by commas.
+
+    Parameters
+    ----------
+    line : str
+        The line to analyze.
+    ncol : int
+        The expected number of columns if line delimited by commas.
+
+    Returns
+    -------
+    has_whitespace : bool
+        Whether the line is delimited by whitespace.
+    has_expected_cols : bool
+        Whether the line has the expected number of columns if delimited by commas.
+    """
+    n_elem = len(next(csv.reader([line])))
+    if n_elem == 1:
+        return True, True
+    elif n_elem == ncol:
+        return False, True
+    else:
+        return False, False
diff --git a/imod/formats/gen/gen.py b/imod/formats/gen/gen.py
index ce2ffde30..cbb908358 100644
--- a/imod/formats/gen/gen.py
+++ b/imod/formats/gen/gen.py
@@ -7,7 +7,7 @@
 import pandas as pd
 from scipy.io import FortranFile, FortranFormattingError
 
-from imod.formats.ipf import _infer_delimwhitespace
+from imod.formats.common import infer_delimwhitespace
 from imod.util.imports import MissingOptionalModule
 
 try:
@@ -52,7 +52,7 @@ def parse_ascii_segments(lines: List[str]):
     indices = np.repeat(np.arange(n_feature), n_vertex)
 
     first_coord = features[0][1:][0]
-    has_whitespace = _infer_delimwhitespace(first_coord, 2)
+    has_whitespace, _ = infer_delimwhitespace(first_coord, 3)
     sep = r"\s+" if has_whitespace else ","
 
     vertex_coords = []
diff --git a/imod/formats/ipf.py b/imod/formats/ipf.py
index e5c8d7cb9..4ffb53b15 100644
--- a/imod/formats/ipf.py
+++ b/imod/formats/ipf.py
@@ -17,20 +17,23 @@
 import pandas as pd
 
 import imod
+from imod.formats.common import infer_delimwhitespace
+from imod.logging import LogLevel
 from imod.util.time import to_pandas_datetime_series
 
 
 def _infer_delimwhitespace(line, ncol):
-    n_elem = len(next(csv.reader([line])))
-    if n_elem == 1:
-        return True
-    elif n_elem == ncol:
-        return False
-    else:
-        warnings.warn(
-            f"Inconsistent IPF: header states {ncol} columns, first line contains {n_elem}"
+    infer_whitespace, has_expected_cols = infer_delimwhitespace(line, ncol)
+
+    if not has_expected_cols:
+        log_message = f"Inconsistent IPF: header states {ncol} columns, first line contains {len(line.split())} whitespace-delimited columns and {len(next(csv.reader([line])))} comma-delimited columns."
+        imod.logging.logger.log(
+            loglevel=LogLevel.WARNING,
+            message=log_message,
+            additional_depth=2,
         )
-        return False
+        warnings.warn(log_message)
+    return infer_whitespace
 
 
 def _read_ipf(path, kwargs=None) -> Tuple[pd.DataFrame, int, str]:
diff --git a/imod/tests/test_formats/test_format_common.py b/imod/tests/test_formats/test_format_common.py
new file mode 100644
index 000000000..cc9f56824
--- /dev/null
+++ b/imod/tests/test_formats/test_format_common.py
@@ -0,0 +1,10 @@
+from imod.formats.common import infer_delimwhitespace
+
+
+def test_infer_delimwhitespace():
+    assert infer_delimwhitespace("1 2 3", 3) == (True, True)
+    assert infer_delimwhitespace("1,2,3", 3) == (False, True)
+    assert infer_delimwhitespace("1,2,3", 4) == (False, False)
+    assert infer_delimwhitespace("1, 2, 3", 3) == (False, True)
+    assert infer_delimwhitespace("1\t2\t3", 3) == (True, True)
+    assert infer_delimwhitespace("1 2,3", 3) == (False, False)