diff --git a/mercurial/cext/parsers.c b/mercurial/cext/parsers.c
--- a/mercurial/cext/parsers.c
+++ b/mercurial/cext/parsers.c
@@ -420,6 +420,14 @@
 		              dirstate_flag_has_meaningful_data |
 		              dirstate_flag_has_file_mtime);
 	}
+	if (t->flags & dirstate_flag_mtime_second_ambiguous) {
+		/* The current code is not able to do the more subtle comparison
+		 * that the MTIME_SECOND_AMBIGUOUS requires. So we ignore the
+		 * mtime */
+		t->flags &= ~(dirstate_flag_mtime_second_ambiguous |
+		              dirstate_flag_has_meaningful_data |
+		              dirstate_flag_has_file_mtime);
+	}
 	t->mode = 0;
 	if (t->flags & dirstate_flag_has_meaningful_data) {
 		if (t->flags & dirstate_flag_mode_exec_perm) {
diff --git a/mercurial/cext/util.h b/mercurial/cext/util.h
--- a/mercurial/cext/util.h
+++ b/mercurial/cext/util.h
@@ -47,6 +47,7 @@
 static const int dirstate_flag_has_fallback_exec = 1 << 12;
 static const int dirstate_flag_fallback_symlink = 1 << 13;
 static const int dirstate_flag_has_fallback_symlink = 1 << 14;
+static const int dirstate_flag_mtime_second_ambiguous = 1 << 15;
 
 extern PyTypeObject dirstateItemType;
 #define dirstate_tuple_check(op) (Py_TYPE(op) == &dirstateItemType)
diff --git a/mercurial/helptext/internals/dirstate-v2.txt b/mercurial/helptext/internals/dirstate-v2.txt
--- a/mercurial/helptext/internals/dirstate-v2.txt
+++ b/mercurial/helptext/internals/dirstate-v2.txt
@@ -390,6 +390,7 @@
     FALLBACK_EXEC = 1 << 12
     HAS_FALLBACK_SYMLINK = 1 << 13
     FALLBACK_SYMLINK = 1 << 14
+    MTIME_SECOND_AMBIGUOUS = 1 << 15
 
   The meaning of each bit is described below.
 
@@ -592,3 +593,10 @@
     this entry should be considered a symlink if that information cannot be
     extracted from the file system. If unset it should be considered a normal
     file instead.
+
+`MTIME_SECOND_AMBIGUOUS`
+    This flag is relevant only when `HAS_FILE_MTIME` is set.  When set, the
+    `mtime` stored in the entry is only valid for comparison with timestamps
+    that have nanosecond information. If available timestamp does not carries
+    nanosecond information, the `mtime` should be ignored and no optimisation
+    can be applied.
diff --git a/mercurial/pure/parsers.py b/mercurial/pure/parsers.py
--- a/mercurial/pure/parsers.py
+++ b/mercurial/pure/parsers.py
@@ -60,6 +60,7 @@
 DIRSTATE_V2_FALLBACK_EXEC = 1 << 12
 DIRSTATE_V2_HAS_FALLBACK_SYMLINK = 1 << 13
 DIRSTATE_V2_FALLBACK_SYMLINK = 1 << 14
+DIRSTATE_V2_MTIME_SECOND_AMBIGUOUS = 1 << 15
 
 
 @attr.s(slots=True, init=False)
@@ -140,6 +141,10 @@
         """Build a new DirstateItem object from V2 data"""
         has_mode_size = bool(flags & DIRSTATE_V2_HAS_MODE_AND_SIZE)
         has_meaningful_mtime = bool(flags & DIRSTATE_V2_HAS_FILE_MTIME)
+        if flags & DIRSTATE_V2_MTIME_SECOND_AMBIGUOUS:
+            # The current code is not able to do the more subtle comparison that the
+            # MTIME_SECOND_AMBIGUOUS requires. So we ignore the mtime
+            has_meaningful_mtime = False
         mode = None
 
         if flags & +DIRSTATE_V2_EXPECTED_STATE_IS_MODIFIED:
diff --git a/rust/hg-core/src/dirstate_tree/on_disk.rs b/rust/hg-core/src/dirstate_tree/on_disk.rs
--- a/rust/hg-core/src/dirstate_tree/on_disk.rs
+++ b/rust/hg-core/src/dirstate_tree/on_disk.rs
@@ -117,6 +117,7 @@
         const FALLBACK_EXEC = 1 << 12;
         const HAS_FALLBACK_SYMLINK = 1 << 13;
         const FALLBACK_SYMLINK = 1 << 14;
+        const MTIME_SECOND_AMBIGUOUS = 1 << 15;
     }
 }
 
@@ -371,6 +372,9 @@
         };
         let mtime = if self.flags().contains(Flags::HAS_FILE_MTIME)
             && !self.flags().contains(Flags::EXPECTED_STATE_IS_MODIFIED)
+            // The current code is not able to do the more subtle comparison that the
+            // MTIME_SECOND_AMBIGUOUS requires. So we ignore the mtime
+            && !self.flags().contains(Flags::MTIME_SECOND_AMBIGUOUS)
         {
             // TODO: replace this by `self.mtime.try_into()?` to use
             // sub-second precision from the file.