diff --git a/reframe/core/config.py b/reframe/core/config.py
index 291c47b3c0..8a5fc009f6 100644
--- a/reframe/core/config.py
+++ b/reframe/core/config.py
@@ -272,7 +272,8 @@ def validate(self):
 
                 partition_names.add(partname)
 
-    def select_subconfig(self, system_fullname=None):
+    def select_subconfig(self, system_fullname=None,
+                         ignore_resolve_errors=False):
         if (self._local_system is not None and
             self._local_system == system_fullname):
             return
@@ -349,25 +350,29 @@ def select_subconfig(self, system_fullname=None):
         required_sections = self._schema['required']
         for name in required_sections:
             if name not in self._local_config.keys():
-                raise ConfigError(f"section '{name}' not defined "
-                                  f"for system '{system_fullname}'")
+                if not ignore_resolve_errors:
+                    raise ConfigError(
+                        f"section '{name}' not defined "
+                        f"for system '{system_fullname}'"
+                    )
 
         # Verify that all environments defined by the system are defined for
         # the current system
-        sys_environs = {
-            *itertools.chain(*(p['environs']
-                               for p in systems[0]['partitions']))
-        }
-        found_environs = {
-            e['name'] for e in self._local_config['environments']
-        }
-        undefined_environs = sys_environs - found_environs
-        if undefined_environs:
-            env_descr = ', '.join(f"'{e}'" for e in undefined_environs)
-            raise ConfigError(
-                f"environments {env_descr} "
-                f"are not defined for '{system_fullname}'"
-            )
+        if not ignore_resolve_errors:
+            sys_environs = {
+                *itertools.chain(*(p['environs']
+                                   for p in systems[0]['partitions']))
+            }
+            found_environs = {
+                e['name'] for e in self._local_config['environments']
+            }
+            undefined_environs = sys_environs - found_environs
+            if undefined_environs:
+                env_descr = ', '.join(f"'{e}'" for e in undefined_environs)
+                raise ConfigError(
+                    f"environments {env_descr} "
+                    f"are not defined for '{system_fullname}'"
+                )
 
         self._local_system = system_fullname
 
diff --git a/reframe/core/systems.py b/reframe/core/systems.py
index 84151fa82e..a288dfaf9a 100644
--- a/reframe/core/systems.py
+++ b/reframe/core/systems.py
@@ -318,8 +318,10 @@ def create(cls, site_config):
                 )
             )
 
-        # Restore configuration
-        site_config.select_subconfig(config_save)
+        # Restore configuration, but ignore unresolved sections or
+        # configuration parameters at the system level; if we came up to this
+        # point, then all is good at the partition level, which is enough.
+        site_config.select_subconfig(config_save, ignore_resolve_errors=True)
         return System(
             name=sysname,
             descr=site_config.get('systems/0/descr'),
diff --git a/reframe/frontend/cli.py b/reframe/frontend/cli.py
index 367b1efa94..7501d1f864 100644
--- a/reframe/frontend/cli.py
+++ b/reframe/frontend/cli.py
@@ -463,7 +463,13 @@ def main():
             site_config = config.load_config(converted)
 
         site_config.validate()
-        site_config.select_subconfig(options.system)
+
+        # We ignore errors about unresolved sections or configuration
+        # parameters here, because they might be defined at the individual
+        # partition level and will be caught when we will instantiating
+        # internally the system and partitions later on.
+        site_config.select_subconfig(options.system,
+                                     ignore_resolve_errors=True)
         for err in options.update_config(site_config):
             printer.warning(str(err))
 
diff --git a/unittests/test_config.py b/unittests/test_config.py
index 9c639e15bd..53f2530a78 100644
--- a/unittests/test_config.py
+++ b/unittests/test_config.py
@@ -201,6 +201,18 @@ def test_select_subconfig_undefined_environment():
         site_config.select_subconfig()
 
 
+def test_select_subconfig_ignore_resolve_errors():
+    site_config = config.load_config('reframe/core/settings.py')
+    site_config['systems'][0]['partitions'][0]['environs'] += ['foo', 'bar']
+    site_config.select_subconfig(ignore_resolve_errors=True)
+
+
+def test_select_subconfig_ignore_no_section_errors():
+    site_config = config.load_config('reframe/core/settings.py')
+    site_config['environments'][0]['target_systems'] = ['foo']
+    site_config.select_subconfig(ignore_resolve_errors=True)
+
+
 def test_select_subconfig():
     site_config = config.load_config('unittests/resources/settings.py')
     site_config.select_subconfig('testsys')