diff --git a/pungi/scripts/create_packages_json.py b/pungi/scripts/create_packages_json.py
index 711a1f99..2a875640 100644
--- a/pungi/scripts/create_packages_json.py
+++ b/pungi/scripts/create_packages_json.py
@@ -19,7 +19,9 @@ import createrepo_c as cr
 import dnf.subject
 import hawkey
 import requests
+import rpm
 import yaml
+from createrepo_c import Package
 from dataclasses import dataclass
 
 
@@ -235,6 +237,20 @@ class PackagesGenerator:
                 os.remove(repomd_record_file_path)
         return list(modules_data)
 
+    @staticmethod
+    def compare_pkgs_version(package_1: Package, package_2: Package) -> int:
+        version_tuple_1 = (
+            package_1.epoch,
+            package_1.version,
+            package_1.release,
+        )
+        version_tuple_2 = (
+            package_2.epoch,
+            package_2.version,
+            package_2.release,
+        )
+        return rpm.labelCompare(version_tuple_1, version_tuple_2)
+
     def generate_packages_json(
             self
     ) -> Dict[AnyStr, Dict[AnyStr, Dict[AnyStr, List[AnyStr]]]]:
@@ -248,6 +264,7 @@ class PackagesGenerator:
                 )
             )
         )
+        all_packages = defaultdict(dict)
         for repo_info in self.repos:
             packages = {}  # type: Dict[AnyStr, cr.Package]
             repomd_records = self._get_repomd_records(
@@ -259,31 +276,50 @@ class PackagesGenerator:
                 packages=packages,
             )
             for package in packages.values():
-                package_name = package.name
-                package_arch = package.arch
+                package_key = f'{package.name}.{package.arch}'
                 if 'module' in package.release:
                     continue
-                if any(re.search(excluded_package, package_name)
-                       for excluded_package in self.excluded_packages):
-                    continue
-                src_package_name = dnf.subject.Subject(
-                    package.rpm_sourcerpm,
-                ).get_nevra_possibilities(
-                    forms=hawkey.FORM_NEVRA,
+                if package_key not in all_packages:
+                    all_packages[package_key]['variant'] = repo_info.name
+                    all_packages[package_key]['arch'] = repo_info.arch
+                    all_packages[package_key]['package'] = package
+                elif self.compare_pkgs_version(
+                        package,
+                        all_packages[package_key]['package']
+                ) > 0:
+                    all_packages[package_key]['variant'] = repo_info.name
+                    all_packages[package_key]['arch'] = repo_info.arch
+                    all_packages[package_key]['package'] = package
+
+        for package_dict in all_packages.values():
+            repo_name = package_dict['variant']
+            repo_arch = package_dict['arch']
+            package = package_dict['package']
+            package_name = package.name
+            package_arch = package.arch
+            if 'module' in package.release:
+                continue
+            if any(re.search(excluded_package, package_name)
+                   for excluded_package in self.excluded_packages):
+                continue
+            src_package_name = dnf.subject.Subject(
+                package.rpm_sourcerpm,
+            ).get_nevra_possibilities(
+                forms=hawkey.FORM_NEVRA,
+            )
+            if len(src_package_name) > 1:
+                # We should stop utility if we can't get exact name of srpm
+                raise ValueError(
+                    'We can\'t get exact name of srpm '
+                    f'by its NEVRA "{package.rpm_sourcerpm}"'
                 )
-                if len(src_package_name) > 1:
-                    # We should stop utility if we can't get exact name of srpm
-                    raise ValueError(
-                        'We can\'t get exact name of srpm '
-                        f'by its NEVRA "{package.rpm_sourcerpm}"'
-                    )
-                else:
-                    src_package_name = src_package_name[0].name
-                    pkgs_list = packages_json[repo_info.name][
-                        repo_info.arch][src_package_name]
-                    added_pkg = f'{package_name}.{package_arch}'
-                if added_pkg not in pkgs_list:
-                    pkgs_list.append(added_pkg)
+            else:
+                src_package_name = src_package_name[0].name
+                pkgs_list = packages_json[repo_name][
+                    repo_arch][src_package_name]
+                added_pkg = f'{package_name}.{package_arch}'
+            if added_pkg not in pkgs_list:
+                pkgs_list.append(added_pkg)
         return packages_json
 
 
diff --git a/tests/test_create_packages_json.py b/tests/test_create_packages_json.py
index ac964e18..f5ffbcf4 100644
--- a/tests/test_create_packages_json.py
+++ b/tests/test_create_packages_json.py
@@ -21,6 +21,14 @@ test_repo_info = RepoInfo(
     is_remote=False,
 )
 
+test_repo_info_2 = RepoInfo(
+    path=FOLDER_WITH_TEST_DATA,
+    folder='test_repo_2',
+    name='TestRepo2',
+    arch='x86_64',
+    is_remote=False,
+)
+
 
 class TestPackagesJson(TestCase):
     def test_01__get_remote_file_content(self):
@@ -53,6 +61,7 @@ class TestPackagesJson(TestCase):
         pg = PackagesGenerator(
             repos=[
                 test_repo_info,
+                test_repo_info_2,
             ],
             excluded_packages=['zziplib-utils'],
         )
@@ -65,9 +74,12 @@ class TestPackagesJson(TestCase):
         )
         test_packages['TestRepo']['x86_64']['zziplib'] = \
             [
-                'zziplib.i686',
                 'zziplib.x86_64',
             ]
+        test_packages['TestRepo2']['x86_64']['zziplib'] = \
+            [
+                'zziplib.i686',
+            ]
         result = pg.generate_packages_json()
         self.assertEqual(
             test_packages,