diff --git a/lxd/rsync/rsync.go b/lxd/rsync/rsync.go
index a4a857abc04c..32f8ffc8c9f2 100644
--- a/lxd/rsync/rsync.go
+++ b/lxd/rsync/rsync.go
@@ -78,8 +78,9 @@ func LocalCopy(source string, dest string, bwlimit string, xattrs bool, rsyncArg
 		"--sparse",
 		"--devices",
 		"--delete",
-		"--checksum",
 		"--numeric-ids",
+		// Checks for file modifications on nanoseconds granularity.
+		"--modify-window=-1",
 	}
 
 	if xattrs {
@@ -316,6 +317,9 @@ func Recv(path string, conn io.ReadWriteCloser, tracker *ioprogress.ProgressTrac
 		"--devices",
 		"--partial",
 		"--sparse",
+		// This flag is only required on the receiving end.
+		// Checks for file modifications on nanoseconds granularity.
+		"--modify-window=-1",
 	}
 
 	if len(features) > 0 {
diff --git a/test/suites/migration.sh b/test/suites/migration.sh
index ed5f4bde20ea..a0a33260e914 100644
--- a/test/suites/migration.sh
+++ b/test/suites/migration.sh
@@ -292,9 +292,49 @@ migration() {
   lxc_remote copy l1:c1 l2:c2 --refresh
   lxc_remote start l2:c2
   lxc_remote file pull l2:c2/root/testfile1 .
+  [ "$(cat testfile1)" = "test" ]
   rm testfile1
   lxc_remote stop -f l2:c2
 
+  # Change the files modification time by adding one nanosecond.
+  # Perform the change on the test runner since the busybox instances `touch` doesn't support setting nanoseconds.
+  lxc_remote start l1:c1
+  c1_pid="$(lxc_remote query l1:/1.0/instances/c1?recursion=1 | jq -r .state.pid)"
+  mtime_old="$(stat -c %y "/proc/${c1_pid}/root/root/testfile1")"
+  mtime_old_ns="$(date -d "$mtime_old" +%N | sed 's/^0*//')"
+
+  # Ensure the final nanoseconds are padded with zeros to create a valid format.
+  mtime_new_ns="$(printf "%09d\n" "$((mtime_old_ns+1))")"
+  mtime_new="$(date -d "$mtime_old" "+%Y-%m-%d %H:%M:%S.${mtime_new_ns} %z")"
+  lxc_remote stop -f l1:c1
+
+  # Before setting the new mtime create a local copy too.
+  lxc_remote copy l1:c1 l1:c2
+
+  # Change the modification time.
+  lxc_remote start l1:c1
+  c1_pid="$(lxc_remote query l1:/1.0/instances/c1?recursion=1 | jq -r .state.pid)"
+  touch -m -d "$mtime_new" "/proc/${c1_pid}/root/root/testfile1"
+  lxc_remote stop -f l1:c1
+
+  # Starting from rsync 3.1.3 it should discover the change of +1 nanosecond.
+  # Check if the file got refreshed to a different remote.
+  lxc_remote copy l1:c1 l2:c2 --refresh
+  lxc_remote start l1:c1 l2:c2
+  c1_pid="$(lxc_remote query l1:/1.0/instances/c1?recursion=1 | jq -r .state.pid)"
+  c2_pid="$(lxc_remote query l2:/1.0/instances/c2?recursion=1 | jq -r .state.pid)"
+  [ "$(stat "/proc/${c1_pid}/root/root/testfile1" -c %y)" = "$(stat "/proc/${c2_pid}/root/root/testfile1" -c %y)" ]
+  lxc_remote stop -f l1:c1 l2:c2
+
+  # Check if the file got refreshed locally.
+  lxc_remote copy l1:c1 l1:c2 --refresh
+  lxc_remote start l1:c1 l1:c2
+  c1_pid="$(lxc_remote query l1:/1.0/instances/c1?recursion=1 | jq -r .state.pid)"
+  c2_pid="$(lxc_remote query l1:/1.0/instances/c2?recursion=1 | jq -r .state.pid)"
+  [ "$(stat "/proc/${c1_pid}/root/root/testfile1" -c %y)" = "$(stat "/proc/${c2_pid}/root/root/testfile1" -c %y)" ]
+  lxc_remote rm -f l1:c2
+  lxc_remote stop -f l1:c1
+
   # This will create snapshot c1/snap0 with test device and expiry date.
   lxc_remote config device add l1:c1 testsnapdev none
   lxc_remote config set l1:c1 snapshots.expiry '1d'