diff --git a/.changeset/patient-mice-greet.md b/.changeset/patient-mice-greet.md
new file mode 100644
index 000000000..efd8cba58
--- /dev/null
+++ b/.changeset/patient-mice-greet.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 1843
+---
+**`init milestone-op` now ignores backlog `999.x` headings when counting milestone phases** — parked backlog items no longer inflate `phase_count` or pin `all_phases_complete` false for an otherwise finished milestone. (#1843)
diff --git a/src/init.cts b/src/init.cts
index 52f2a576f..1a2294bab 100644
--- a/src/init.cts
+++ b/src/init.cts
@@ -1189,6 +1189,7 @@ function cmdInitMilestoneOp(cwd: string, raw: boolean): void {
     const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:/gi;
     let m: RegExpExecArray | null;
     while ((m = phasePattern.exec(currentSection)) !== null) {
+      if (/^999(?:\.|$)/.test(m[1])) continue;
       roadmapPhaseNumbers.push(m[1]);
     }
   } catch {
diff --git a/tests/init.test.cjs b/tests/init.test.cjs
index e665e0281..871786122 100644
--- a/tests/init.test.cjs
+++ b/tests/init.test.cjs
@@ -976,6 +976,7 @@ describe('cmdInitMilestoneOp', () => {
       path.join(tmpDir, '.planning', 'config.json'),
       JSON.stringify({ project_code: 'PROJ' }, null, 2)
     );
+
     fs.writeFileSync(
       path.join(tmpDir, '.planning', 'STATE.md'),
       [
@@ -1008,6 +1009,47 @@ describe('cmdInitMilestoneOp', () => {
     assert.strictEqual(output.all_phases_complete, true);
   });
 
+  test('backlog 999.x headings do not inflate milestone phase counts (#1838)', () => {
+    const phase1 = path.join(tmpDir, '.planning', 'phases', '01-setup');
+    fs.mkdirSync(phase1, { recursive: true });
+    fs.writeFileSync(path.join(phase1, '01-01-PLAN.md'), '# Plan');
+    fs.writeFileSync(path.join(phase1, '01-01-SUMMARY.md'), '# Summary');
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'STATE.md'),
+      [
+        '---',
+        'gsd_state_version: 1.0',
+        'milestone: v1.0.0',
+        'milestone_name: Test Milestone',
+        'status: completed',
+        '---',
+        '',
+      ].join('\n')
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      [
+        '# Roadmap',
+        '',
+        '## 🚧 v1.0.0 Test Milestone',
+        '### Phase 1: Setup',
+        '',
+        '## Backlog',
+        '### Phase 999.1: Deferred Idea',
+        '### Phase 999.2: Another Deferred Idea',
+        '',
+      ].join('\n')
+    );
+
+    const result = runGsdTools('init milestone-op', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.phase_count, 1);
+    assert.strictEqual(output.completed_phases, 1);
+    assert.strictEqual(output.all_phases_complete, true);
+  });
+
   test('archive directory scanning', () => {
     fs.mkdirSync(path.join(tmpDir, '.planning', 'archive', 'v1.0'), { recursive: true });
     fs.mkdirSync(path.join(tmpDir, '.planning', 'archive', 'v0.9'), { recursive: true });