Owners and officers with greater than two-percent share of a Subchapter S corporation, or partners in a partnership or LLC, cannot make pre-tax contributions to their HSAs by salary reduction. Any contributions made to their HSAs by the company are taxable as income. However, they can make their own personal contributions to their HSAs and claim the contributed amount as a deduction on their personal income taxes.
Source: American Benefits Group https://www.amben.com/demos/marketing/HSA_Employer_FAQ.pdf
Ameriflex also has an article answering this question: https://www.myameriflex.com/faqs/54-can-business-owners-make-pre-tax-contributions-to-hsas
