diff --git a/debian/tests/system-test b/debian/tests/system-test
index cb7ad6da..72055c7d 100755
--- a/debian/tests/system-test
+++ b/debian/tests/system-test
@@ -6,14 +6,29 @@ set -eux
 
 . debian/tests/setup
 
-# FIXME: investigate more why those fail
-# FIXME: look into filters to cleanly disable problematic tests
-rm ${APTLY_SRC_DIR}/system/t02_config/config.py
-rm ${APTLY_SRC_DIR}/system/t07_serve/serve.py
-rm ${APTLY_SRC_DIR}/system/t12_api/docs.py
-rm ${APTLY_SRC_DIR}/system/t14_graph/graph.py
+## env
+TESTS_DIR="${APTLY_SRC_DIR}/system"
 
-# etcd fixture is arch-specific
-rm -fr ${APTLY_SRC_DIR}/system/t13_etcd
+## functions
+disable_test() {
+  local file=${1}.py
+  local name=$2
+  local reason=$3
+
+  echo "${name}.skipTest = 'Debian autopkgtest: $reason'" >> ${TESTS_DIR}/${file}
+}
+
+## main
+export USER=root # for t07/RootDirInaccessible
+
+disable_test t02_config/config CreateConfigTest "different conf"
+disable_test t04_mirror/create CreateMirror35Test "flaky on s390"
+disable_test t07_serve/serve Serve1Test "minor html diff"
+disable_test t12_api/docs TaskAPITestSwaggerDocs "no recent swag"
+disable_test t14_graph/graph CreateGraphTest "no viewer"
+disable_test t14_graph/graph CreateGraphOutputTest "no viewer"
+
+# etcd fixture is entirely arch-specific
+rm -fr ${TESTS_DIR}/t13_etcd
 
 make -C $APTLY_SRC_DIR system-test