diff --git a/src/utils/pydantic_ai_helpers.py b/src/utils/pydantic_ai_helpers.py
index ddbbf65cd..607d33da2 100644
--- a/src/utils/pydantic_ai_helpers.py
+++ b/src/utils/pydantic_ai_helpers.py
@@ -54,6 +54,7 @@ def _skills_capability(
     return SkillsCapability(
         directories=[str(path) for path in skills_config.paths],
         validate=False,
+        exclude_tools=["run_skill_script"],
     )
 
 
diff --git a/tests/e2e/features/skills.feature b/tests/e2e/features/skills.feature
index baec0a0be..3d919828c 100644
--- a/tests/e2e/features/skills.feature
+++ b/tests/e2e/features/skills.feature
@@ -101,37 +101,6 @@ Feature: Agent skills tests
             "toolgroup_id": "builtin::agent-skills",
             "server_source": "builtin",
             "type": "tool"
-          },
-          {
-            "identifier": "run_skill_script",
-            "description": "Execute a skill script that performs actions or computations.\n\nScripts are executable programs provided by skills that can perform actions\n(API calls, file operations), process data (transformations, analysis), or\ngenerate outputs (reports, visualizations).\n\nWhen to use this:\n- When a skill's instructions tell you to run a specific script\n- To perform automated tasks that the skill provides\n- For data processing, API interactions, or file operations",
-            "parameters": [
-              {
-                "name": "skill_name",
-                "description": "Name of the skill containing the script.",
-                "parameter_type": "string",
-                "required": true,
-                "default": null
-              },
-              {
-                "name": "script_name",
-                "description": "Exact name of the script as listed in the skill.\nExamples: \"analyze.py\", \"scripts/analyze.py\", \"scripts/deploy.sh\", \"scripts/runner\"\nMust match exactly - do not infer or guess.",
-                "parameter_type": "string",
-                "required": true,
-                "default": null
-              },
-              {
-                "name": "args",
-                "description": "Arguments required by the script.\nKeys must match the parameter names in the script's schema.",
-                "parameter_type": "object",
-                "required": false,
-                "default": null
-              }
-            ],
-            "provider_id": "agent-skills",
-            "toolgroup_id": "builtin::agent-skills",
-            "server_source": "builtin",
-            "type": "tool"
           }
         ]
       }
diff --git a/tests/unit/app/endpoints/test_tools.py b/tests/unit/app/endpoints/test_tools.py
index 1a0e9ff41..1403997b5 100644
--- a/tests/unit/app/endpoints/test_tools.py
+++ b/tests/unit/app/endpoints/test_tools.py
@@ -353,7 +353,6 @@ async def test_tools_endpoint_includes_agent_capability_tools(
     assert "list_skills" in tool_ids
     assert "load_skill" in tool_ids
     assert "read_skill_resource" in tool_ids
-    assert "run_skill_script" in tool_ids
 
     list_skills = next(
         tool for tool in response.tools if tool.identifier == "list_skills"
diff --git a/tests/unit/utils/test_pydantic_ai.py b/tests/unit/utils/test_pydantic_ai.py
index 2ed416dea..39c2a19e0 100644
--- a/tests/unit/utils/test_pydantic_ai.py
+++ b/tests/unit/utils/test_pydantic_ai.py
@@ -458,7 +458,6 @@ def test_returns_skills_tools_when_configured(
             "list_skills",
             "load_skill",
             "read_skill_resource",
-            "run_skill_script",
         ]
         assert all(
             tool.provider_id == "agent-skills"