"An individual who is eligible to receive medical services at an IHS facility, but who has not actually received such services during the previous three months, is an eligible individual within the meaning of § 223(c)(1) who may establish and make tax-free contributions to an HSA. However, an individual generally is not an eligible individual if the individual has received medical services at an IHS facility at any time during the previous three months. Notice 2004-2, Q&A-6, provides that the receipt of permitted coverage, such as dental and vision care, or the receipt of preventive care, such as well-baby visits, immunizations, weight-loss and tobacco cessation programs, does not affect an individual’s eligibility."
For the full publication, http://www.irs.gov/irb/2012-08_IRB/ar11.html
In summary, if you are eligible to receive benefits from an IHS facility then it does not necessarily make you ineligible for the HSA. However, if you have received any benefit from an IHS facility (*except for allowable care as described below) then you are ineligible for personal or employer contributions to your HSA for the 3 months following the medical service. You should let your employer know that you used the IHS facility, so that they do not contribute funds that you are ineligible to receive according to IRS rules.
*Use of the IHS facility for dental, vision, preventative, well-baby visits, immunizations, weight-loss and tobacco cessation will not affect your HSA eligibility in any way.