diff --git a/src/agents/copilot-runner.ts b/src/agents/copilot-runner.ts
index 252708ccd43c0..91966cab133af 100644
--- a/src/agents/copilot-runner.ts
+++ b/src/agents/copilot-runner.ts
@@ -67,9 +67,17 @@ export async function runCopilotCliAgent(params: {
   const modelId = backendConfig ? normalizeCliModel(rawModelId, backendConfig.config) : rawModelId;
   const modelDisplay = `copilot-cli/${modelId}`;
 
+  // Resolve tool filters from backend config
+  const toolConfig = backendConfig?.config as Record<string, unknown> | undefined;
+  const availableTools = (toolConfig?.availableTools as string[] | undefined) ?? undefined;
+  const excludedTools = (toolConfig?.excludedTools as string[] | undefined) ?? undefined;
+  const hasToolFilters = !!(availableTools?.length || excludedTools?.length);
+
   const extraSystemPrompt = [
     params.extraSystemPrompt?.trim(),
-    "Tools are disabled in this session. Do not call tools.",
+    // Only append the blanket "tools disabled" message when no SDK-level tool
+    // filters are configured — in that case tools really are fully disabled.
+    ...(!hasToolFilters ? ["Tools are disabled in this session. Do not call tools."] : []),
   ]
     .filter(Boolean)
     .join("\n");
@@ -121,6 +129,8 @@ export async function runCopilotCliAgent(params: {
       systemPrompt,
       timeoutMs: params.timeoutMs,
       sessionId: params.cliSessionId,
+      availableTools,
+      excludedTools,
     });
 
     const text = result.text?.trim();
diff --git a/src/agents/copilot-sdk.test.ts b/src/agents/copilot-sdk.test.ts
index 593a680949cc8..581265a331a32 100644
--- a/src/agents/copilot-sdk.test.ts
+++ b/src/agents/copilot-sdk.test.ts
@@ -181,6 +181,63 @@ describe("copilot-sdk", () => {
       expect(mockClient.stop).toHaveBeenCalled();
     });
 
+    it("passes availableTools to session config and auto-approves permissions", async () => {
+      mockSession.sendAndWait.mockResolvedValueOnce({
+        data: { content: "tools!" },
+      });
+
+      const { runCopilotAgent } = await import("./copilot-sdk.js");
+      await runCopilotAgent({
+        prompt: "use tools",
+        availableTools: ["read", "write", "exec"],
+        timeoutMs: 5_000,
+      });
+
+      const sessionConfig = mockClient.createSession.mock.calls[0]?.[0];
+      expect(sessionConfig.availableTools).toEqual(["read", "write", "exec"]);
+      expect(sessionConfig.excludedTools).toBeUndefined();
+      // Permission handler should auto-approve when tool filters are set
+      const permResult = await sessionConfig.onPermissionRequest();
+      expect(permResult.kind).toBe("approved");
+    });
+
+    it("passes excludedTools to session config and auto-approves permissions", async () => {
+      mockSession.sendAndWait.mockResolvedValueOnce({
+        data: { content: "tools!" },
+      });
+
+      const { runCopilotAgent } = await import("./copilot-sdk.js");
+      await runCopilotAgent({
+        prompt: "use tools",
+        excludedTools: ["exec", "write"],
+        timeoutMs: 5_000,
+      });
+
+      const sessionConfig = mockClient.createSession.mock.calls[0]?.[0];
+      expect(sessionConfig.excludedTools).toEqual(["exec", "write"]);
+      expect(sessionConfig.availableTools).toBeUndefined();
+      const permResult = await sessionConfig.onPermissionRequest();
+      expect(permResult.kind).toBe("approved");
+    });
+
+    it("denies permissions when no tool filters are set", async () => {
+      mockSession.sendAndWait.mockResolvedValueOnce({
+        data: { content: "no tools" },
+      });
+
+      const { runCopilotAgent } = await import("./copilot-sdk.js");
+      await runCopilotAgent({
+        prompt: "hi",
+        timeoutMs: 5_000,
+      });
+
+      const sessionConfig = mockClient.createSession.mock.calls[0]?.[0];
+      expect(sessionConfig.availableTools).toBeUndefined();
+      expect(sessionConfig.excludedTools).toBeUndefined();
+      const permResult = await sessionConfig.onPermissionRequest();
+      expect(permResult.kind).toBe("denied-interactively-by-user");
+    });
+
     it("passes system prompt as append mode", async () => {
       mockSession.sendAndWait.mockResolvedValueOnce({
         data: { content: "Got it." },
diff --git a/src/agents/copilot-sdk.ts b/src/agents/copilot-sdk.ts
index 067dffbb9c0b9..a62f2ece9c526 100644
--- a/src/agents/copilot-sdk.ts
+++ b/src/agents/copilot-sdk.ts
@@ -116,6 +116,10 @@ export type CopilotAgentRunOptions = {
   systemPrompt?: string;
   timeoutMs?: number;
   sessionId?: string;
+  /** SDK-level tool allowlist — only these tools are available (takes precedence over excludedTools). */
+  availableTools?: string[];
+  /** SDK-level tool blocklist — all tools except these are available. */
+  excludedTools?: string[];
 };
 
 export type CopilotAgentRunResult = {
@@ -139,18 +143,31 @@ export async function runCopilotAgent(
   try {
     await ensureAuthenticated(client);
 
+    const hasToolFilters = !!(options.availableTools?.length || options.excludedTools?.length);
+
     const sessionConfig: SessionConfig = {
       model: options.model,
       workingDirectory: options.workspaceDir,
       streaming: true,
-      // Deny tool-use permission requests by default (security: callers must
-      // opt-in to specific capabilities through session configuration).
-      onPermissionRequest: async () => ({
-        kind: "denied-interactively-by-user",
-        feedback: "Tool use is not permitted in this session.",
-      }),
+      ...(options.availableTools?.length && { availableTools: options.availableTools }),
+      ...(options.excludedTools?.length && { excludedTools: options.excludedTools }),
+      // When tool filters are configured, auto-approve permission requests since
+      // the SDK enforces the allowlist/blocklist. Otherwise deny all by default.
+      onPermissionRequest: hasToolFilters
+        ? async () => ({ kind: "approved" as const })
+        : async () => ({
+            kind: "denied-interactively-by-user" as const,
+            feedback: "Tool use is not permitted in this session.",
+          }),
     };
 
+    if (hasToolFilters) {
+      log.info("copilot session tool filters configured", {
+        availableTools: options.availableTools,
+        excludedTools: options.excludedTools,
+      });
+    }
+
     if (options.systemPrompt) {
       sessionConfig.systemMessage = {
         mode: "append",