diff --git a/.github/scripts/check-zombienet-flaky-tests.sh b/.github/scripts/check-zombienet-flaky-tests.sh
index a654841e530ff..98a0e09a7a04c 100755
--- a/.github/scripts/check-zombienet-flaky-tests.sh
+++ b/.github/scripts/check-zombienet-flaky-tests.sh
@@ -28,11 +28,11 @@ line_num=0
 
 while IFS= read -r line || [[ -n "$line" ]]; do
     line_num=$((line_num + 1))
-    
+
     if [[ -z "$line" ]]; then
         continue
     fi
-    
+
     # Parse format: test-name:issue-number
     if [[ ! "$line" =~ ^([^:]+):([0-9]+)$ ]]; then
         echo "❌ Line $line_num: Missing required issue number" >&2
@@ -42,26 +42,26 @@ while IFS= read -r line || [[ -n "$line" ]]; do
         has_errors=true
         continue
     fi
-    
+
     test_name="${BASH_REMATCH[1]}"
     issue_number="${BASH_REMATCH[2]}"
-    
+
     set +e
     issue_data=$(gh issue view "$issue_number" --json state,title,url 2>&1)
     gh_exit_code=$?
     set -e
-    
+
     if [[ $gh_exit_code -ne 0 ]]; then
         echo "❌ Line $line_num: Issue #$issue_number does not exist" >&2
         echo "   Test: $test_name" >&2
         has_errors=true
         continue
     fi
-    
+
     url=$(echo "$issue_data" | jq -r '.url')
     state=$(echo "$issue_data" | jq -r '.state')
     title=$(echo "$issue_data" | jq -r '.title')
-    
+
     # Check if it's an issue (not a PR) by verifying the URL contains '/issues/'
     if [[ ! "$url" =~ /issues/ ]]; then
         echo "❌ Line $line_num: #$issue_number is a Pull Request, not an Issue" >&2
@@ -71,7 +71,7 @@ while IFS= read -r line || [[ -n "$line" ]]; do
         has_errors=true
         continue
     fi
-    
+
     if [[ "$state" == "OPEN" ]]; then
         echo "✅ Line $line_num: $test_name -> Issue #$issue_number (open)"
     else
@@ -79,8 +79,9 @@ while IFS= read -r line || [[ -n "$line" ]]; do
         echo "   Test: $test_name" >&2
         echo "   Consider removing this entry if the issue is resolved." >&2
     fi
-    
-done < "$FLAKY_TESTS_FILE"
+
+# exclude empty lines and comments
+done < <(grep -vE '^\s*(#|$)' "$FLAKY_TESTS_FILE")
 
 echo
 
diff --git a/.github/zombienet-flaky-tests b/.github/zombienet-flaky-tests
index e3c171f9ee671..c22ca3bbd2c6f 100644
--- a/.github/zombienet-flaky-tests
+++ b/.github/zombienet-flaky-tests
@@ -9,3 +9,10 @@ zombienet-substrate-0002-validators-warp-sync:8871
 zombienet-cumulus-0009-elastic_scaling_pov_recovery:8986
 zombienet-cumulus-0010-elastic_scaling_multiple_block_per_slot:8999
 zombienet-polkadot-functional-0014-chunk-fetching-network-compatibility:9980
+# disabled until zombienet support penpal (https://github.com/paritytech/zombienet-sdk/issues/480)
+zombienet-polkadot-shared-core-idle-parachain:10653
+zombienet-polkadot-functional-async-backing-6-seconds-rate:10653
+zombienet-polkadot-elastic-scaling-doesnt-break-parachains:10653
+zombienet-polkadot-smoke-0005-precompile-pvf-smoke:10653
+zombienet-polkadot-smoke-0004-coretime-smoke-test:10653
+zombienet-polkadot-smoke-0002-parachains-parachains-upgrade-smoke:10653