diff --git a/cmd/k3s/main.go b/cmd/k3s/main.go
index 52d5cefbf62e..90eae7268eab 100644
--- a/cmd/k3s/main.go
+++ b/cmd/k3s/main.go
@@ -8,6 +8,7 @@ import (
 	"os"
 	"os/exec"
 	"path/filepath"
+	"slices"
 	"strconv"
 	"strings"
 
@@ -27,6 +28,7 @@ import (
 )
 
 var criDefaultConfigPath = "/etc/crictl.yaml"
+var externalCLIActions = []string{"crictl", "ctr", "kubectl"}
 
 // main entrypoint for the k3s multicall binary
 func main() {
@@ -105,7 +107,7 @@ func findDebug(args []string) bool {
 	if debug {
 		return debug
 	}
-	debug, _ = strconv.ParseBool(configfilearg.MustFindString(args, "debug"))
+	debug, _ = strconv.ParseBool(configfilearg.MustFindString(args, "debug", externalCLIActions...))
 	return debug
 }
 
@@ -125,7 +127,7 @@ func findDataDir(args []string) string {
 	if dataDir != "" {
 		return dataDir
 	}
-	dataDir = configfilearg.MustFindString(args, "data-dir")
+	dataDir = configfilearg.MustFindString(args, "data-dir", externalCLIActions...)
 	if d, err := datadir.Resolve(dataDir); err == nil {
 		dataDir = d
 	} else {
@@ -143,7 +145,7 @@ func findPreferBundledBin(args []string) bool {
 	fs.SetOutput(io.Discard)
 	fs.BoolVar(&preferBundledBin, "prefer-bundled-bin", false, "Prefer bundled binaries")
 
-	preferRes := configfilearg.MustFindString(args, "prefer-bundled-bin")
+	preferRes := configfilearg.MustFindString(args, "prefer-bundled-bin", externalCLIActions...)
 	if preferRes != "" {
 		preferBundledBin, _ = strconv.ParseBool(preferRes)
 	}
@@ -158,8 +160,7 @@ func findPreferBundledBin(args []string) bool {
 // it returns false so that standard CLI wrapping can occur.
 func runCLIs(dataDir string) bool {
 	progName := filepath.Base(os.Args[0])
-	switch progName {
-	case "crictl", "ctr", "kubectl":
+	if slices.Contains(externalCLIActions, progName) {
 		if err := externalCLI(progName, dataDir, os.Args[1:]); err != nil && !errors.Is(err, context.Canceled) {
 			logrus.Fatal(err)
 		}
diff --git a/pkg/configfilearg/defaultparser.go b/pkg/configfilearg/defaultparser.go
index b9b6d04fca2c..85d553bc08e8 100644
--- a/pkg/configfilearg/defaultparser.go
+++ b/pkg/configfilearg/defaultparser.go
@@ -1,6 +1,8 @@
 package configfilearg
 
 import (
+	"slices"
+
 	"github.com/k3s-io/k3s/pkg/cli/cmds"
 	"github.com/k3s-io/k3s/pkg/version"
 	"github.com/sirupsen/logrus"
@@ -23,15 +25,31 @@ func MustParse(args []string) []string {
 	return result
 }
 
-func MustFindString(args []string, target string) string {
+func MustFindString(args []string, target string, commandsWithoutOverride ...string) string {
+	overrideFlags := []string{"--help", "-h", "--version", "-v"}
+	// Check to see if the command or subcommand being executed supports override flags.
+	// Some subcommands such as `k3s ctr` or just `ctr` need to be extracted out even to
+	// provide version or help text, and we cannot short-circuit loading the config file. For
+	// these commands, treat failure to load the config file as a warning instead of a fatal.
+	if len(args) > 0 && args[0] == version.Program {
+		args = args[1:]
+	}
+	if len(args) > 0 && slices.Contains(commandsWithoutOverride, args[0]) {
+		overrideFlags = nil
+	}
+
 	parser := &Parser{
-		OverrideFlags: []string{"--help", "-h", "--version", "-v"},
+		OverrideFlags: overrideFlags,
 		EnvName:       version.ProgramUpper + "_CONFIG_FILE",
 		DefaultConfig: "/etc/rancher/" + version.Program + "/config.yaml",
 	}
 	result, err := parser.FindString(args, target)
 	if err != nil {
-		logrus.Fatal(err)
+		if len(overrideFlags) > 0 {
+			logrus.Fatal(err)
+		} else {
+			logrus.Warn(err)
+		}
 	}
 	return result
 }
diff --git a/pkg/configfilearg/defaultparser_test.go b/pkg/configfilearg/defaultparser_test.go
index 8ae8decc26fa..92002a8cb04a 100644
--- a/pkg/configfilearg/defaultparser_test.go
+++ b/pkg/configfilearg/defaultparser_test.go
@@ -85,7 +85,7 @@ func Test_UnitMustFindString(t *testing.T) {
 	}{
 		{
 			name:   "Target not found in config file",
-			args:   []string{"--foo", "bar"},
+			args:   []string{"k3s", "--foo", "bar"},
 			target: "token",
 
 			want: "",
@@ -95,7 +95,7 @@ func Test_UnitMustFindString(t *testing.T) {
 		},
 		{
 			name:   "Target found in config file",
-			args:   []string{"--foo", "bar"},
+			args:   []string{"k3s", "--foo", "bar"},
 			target: "token",
 
 			want: "12345",
@@ -104,11 +104,31 @@ func Test_UnitMustFindString(t *testing.T) {
 			teardown: func() error { return os.Unsetenv("K3S_CONFIG_FILE") },
 		},
 		{
-			name:   "Override flag found, function is short-circuited",
-			args:   []string{"--foo", "bar", "-h"},
+			name:   "Override flag is returned if found",
+			args:   []string{"k3s", "--foo", "bar", "--version"},
 			target: "token",
 
-			want: "-h",
+			want: "--version",
+
+			setup:    func() error { return os.Setenv("K3S_CONFIG_FILE", "./testdata/defaultdata.yaml") },
+			teardown: func() error { return os.Unsetenv("K3S_CONFIG_FILE") },
+		},
+		{
+			name:   "Override flag is not returned for specific subcommands",
+			args:   []string{"k3s", "ctr", "--foo", "bar", "--version"},
+			target: "token",
+
+			want: "12345",
+
+			setup:    func() error { return os.Setenv("K3S_CONFIG_FILE", "./testdata/defaultdata.yaml") },
+			teardown: func() error { return os.Unsetenv("K3S_CONFIG_FILE") },
+		},
+		{
+			name:   "Override flag is not returned for specific subcommands",
+			args:   []string{"kubectl", "--foo", "bar", "--help"},
+			target: "token",
+
+			want: "12345",
 
 			setup:    func() error { return os.Setenv("K3S_CONFIG_FILE", "./testdata/defaultdata.yaml") },
 			teardown: func() error { return os.Unsetenv("K3S_CONFIG_FILE") },
@@ -121,7 +141,9 @@ func Test_UnitMustFindString(t *testing.T) {
 				t.Errorf("Setup for MustFindString() failed = %v", err)
 				return
 			}
-			if got := MustFindString(tt.args, tt.target); got != tt.want {
+			got := MustFindString(tt.args, tt.target, "crictl", "ctr", "kubectl")
+			t.Logf("MustFindString(%+v, %+v) = %s", tt.args, tt.target, got)
+			if got != tt.want {
 				t.Errorf("MustFindString() = %+v\nWant = %+v", got, tt.want)
 			}
 		})