In general, telemedicine visits are not considered “qualified visits” for facilities paid under a prospective payment system (like FQHCs and RHCs), because they are not face-to-face.
Here are the Medicare rules about what constitutes qualified visits for FQHCs and also for RHCs.
What is confusing is that now 9921x (which are on the list of qualifying services) can now be billed with modifier -95. Unfortunately, while the code is on the list, they are still not face-to-face.
Medicare did create a Virtual Communications HCPCS code (G0071) which is intended to be used like the virtual check-in codes (G2010, G2012.) Here’s an FAQ on FQHC & RHC use of virtual communication codes.
Medicaid (and CHIP) are slightly different. Each state’s State Medicaid Agency can agree to make telemedicine encounters paid on the flat visit PPS rate. However, this first requires submission and approval of a CMS state plan amendment (SPA.) [see page 10, question 6.] Unfortunately, 2/3 of states have not yet done this.
Best bet: contact your state’s FQHC division and ask; get the answer in writing.