diff --git a/cmd/gen.go b/cmd/gen.go
index 3842f02b37d..97bd6342f1e 100644
--- a/cmd/gen.go
+++ b/cmd/gen.go
@@ -46,11 +46,6 @@ var genCmd = cli.Command{
 			config.SchemaStr[filename] = string(schemaRaw)
 		}
 
-		if err = config.Check(); err != nil {
-			fmt.Fprintln(os.Stderr, "invalid config format: "+err.Error())
-			os.Exit(1)
-		}
-
 		err = codegen.Generate(*config)
 		if err != nil {
 			fmt.Fprintln(os.Stderr, err.Error())
diff --git a/cmd/init.go b/cmd/init.go
index 1e7c18b9327..6ad7e58c811 100644
--- a/cmd/init.go
+++ b/cmd/init.go
@@ -78,11 +78,6 @@ func GenerateGraphServer(config *codegen.Config, serverFilename string) {
 		config.SchemaStr[filename] = string(schemaRaw)
 	}
 
-	if err := config.Check(); err != nil {
-		fmt.Fprintln(os.Stderr, "invalid config format: "+err.Error())
-		os.Exit(1)
-	}
-
 	if err := codegen.Generate(*config); err != nil {
 		fmt.Fprintln(os.Stderr, err.Error())
 		os.Exit(1)
diff --git a/codegen/codegen.go b/codegen/codegen.go
index 773e3db7cc4..8aadd48cd2d 100644
--- a/codegen/codegen.go
+++ b/codegen/codegen.go
@@ -1,6 +1,7 @@
 package codegen
 
 import (
+	"fmt"
 	"log"
 	"os"
 	"path/filepath"
@@ -19,6 +20,9 @@ func Generate(cfg Config) error {
 		return err
 	}
 
+	if err := cfg.check(); err != nil {
+		return fmt.Errorf("invalid config format: " + err.Error())
+	}
 	_ = syscall.Unlink(cfg.Exec.Filename)
 	_ = syscall.Unlink(cfg.Model.Filename)
 
diff --git a/codegen/config.go b/codegen/config.go
index 4319953ba18..9826ca5dfe5 100644
--- a/codegen/config.go
+++ b/codegen/config.go
@@ -178,7 +178,7 @@ func (c *PackageConfig) IsDefined() bool {
 	return c.Filename != ""
 }
 
-func (cfg *Config) Check() error {
+func (cfg *Config) check() error {
 	if err := cfg.Models.Check(); err != nil {
 		return errors.Wrap(err, "config.models")
 	}
@@ -200,36 +200,18 @@ func (cfg *Config) Check() error {
 		cfg.Resolver,
 	}
 	filesMap := make(map[string]bool)
-	pkgConfigsByDir := make(map[string][]PackageConfig)
-	for i, current := range packageConfigList {
-		if i == 0 {
-			filesMap[current.Filename] = true
-			pkgConfigsByDir[current.Dir()] = []PackageConfig{current}
-			continue
-		}
+	pkgConfigsByDir := make(map[string]PackageConfig)
+	for _, current := range packageConfigList {
 		_, fileFound := filesMap[current.Filename]
 		if fileFound {
 			return fmt.Errorf("filename %s defined more than once", current.Filename)
 		}
 		filesMap[current.Filename] = true
-		prevPkgList, inSameDir := pkgConfigsByDir[current.Dir()]
-		if inSameDir {
-			for _, previous := range prevPkgList {
-				if current.Package != previous.Package {
-					eitherPackageEmpty := previous.Package != "" || current.Package != ""
-					if eitherPackageEmpty {
-						if current.Package == filepath.Base(current.Dir()) && previous.Package == "" {
-							break
-						}
-						if previous.Package == filepath.Base(previous.Dir()) && current.Package == "" {
-							break
-						}
-						return fmt.Errorf("filenames %s and %s are in the same directory but have different package definitions", current.Filename, previous.Filename)
-					}
-				}
-			}
+		previous, inSameDir := pkgConfigsByDir[current.Dir()]
+		if inSameDir && current.Package != previous.Package {
+			return fmt.Errorf("filenames %s and %s are in the same directory but have different package definitions", stripPath(current.Filename), stripPath(previous.Filename))
 		}
-		pkgConfigsByDir[current.Dir()] = append(pkgConfigsByDir[current.Dir()], current)
+		pkgConfigsByDir[current.Dir()] = current
 	}
 
 	return nil
@@ -312,3 +294,7 @@ func findCfgInDir(dir string) string {
 	}
 	return ""
 }
+
+func stripPath(path string) string {
+	return filepath.Base(path)
+}