diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index 60fd2ab..e9ffe4f 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -229,7 +229,7 @@ jobs:
       # future changes to setup-nextstrain-cli.
       #
       #   -trs, 28 April 2022
-      - uses: nextstrain/.github/actions/setup-nextstrain-cli@1fbb3f2e3bf29374d2706f720f65d4025853a89a
+      - uses: nextstrain/.github/actions/setup-nextstrain-cli@4366771cea2482d31395ad9b5d351b950daa798d
         with:
           runtime: ${{ matrix.runtime }}
           # Consider parameterizing the Python version. -trs, 1 April 2022
diff --git a/actions/setup-nextstrain-cli/action.yaml b/actions/setup-nextstrain-cli/action.yaml
index facfa42..def4f03 100644
--- a/actions/setup-nextstrain-cli/action.yaml
+++ b/actions/setup-nextstrain-cli/action.yaml
@@ -65,9 +65,10 @@ runs:
       env:
         runtime: ${{ inputs.runtime }}
 
-    - run: nextstrain update
+    # TODO: Remove this once https://github.com/nextstrain/cli/issues/318 is resolved.
+    - if: inputs.runtime == 'conda'
+      run: nextstrain update
       shell: bash
-      continue-on-error: true
 
     - run: nextstrain version --verbose
       shell: bash