Like @ shin-haeng-kang, setting a signup_enabled: false for a new user in the siteβs settings and creating users from the admin menu, and then editing the password after creating the user will work.
If users already exist, I found the following issue on the issue , which shows how to manually edit the postgres database.
From gitlab server:
sudo -u git -H psql -d gitlabhq_production gitlabhq_production=> update users set confirmation_token=null, confirmed_at=now() where confirmed_at is null;
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