Medicaid 1099 Forms for NEMT Providers: Box 6, Mismatches, and Corrections

What the Medicaid 1099 reports

Medicaid payments are business income, and the payer tells the IRS about them. The IRS instructions (revised December 2026) put medical and health care payments in box 6 of Form 1099-MISC: payments to each physician or other supplier or provider of medical or health care services, including payments by health insurers. Publication 1099 for 2026 says these forms come mainly from medical assistance programs and health plans, and the instructions add that payments by federal, state, and local agencies are reportable. South Carolina’s Medicaid agency, for one, reported its 2023 provider payments in box 6 (provider bulletin, January 22, 2024).

Four rules decide whether you get one and what it says:

• The $2,000 floor. Starting with 2026 payments, a payer files a box 6 form once it pays you $2,000 or more in a year. The floor was $600 before, and the IRS will adjust it for inflation starting in 2027 (Publication 1099, 2026).
• Corporations are included. The usual exemption for payments to corporations does not apply to box 6, so an LLC taxed as an S corporation still gets one.
• One form per payer. The state agency reports fee-for-service payments, and each health plan reports its own. A broker that pays your claims is a separate payer, so ask its provider services team which form and box it uses.
• Your tax ID and legal name come from your W-9. Indiana, for example, reports every payment made to a tax ID, under the legal name on the W-9 in your enrollment packet (IHCP module, version 7.0, March 13, 2025). Indiana tells providers to keep that information current in their provider profile, so a stale name or number does not end up on the form.

Why your Medicaid 1099 does not match your books

The form follows the money, not the trip. Under IRS rules, an amount counts as paid when it is credited to you and made available for you to draw on (26 CFR 1.6041-1(h)). Pennsylvania’s FAQ says its 1099 total equals the year-to-date balance on the last remittance advice of the year, added up across all your service locations.

Here is a billing example. Say you drove $52,000 of Medicaid trips in 2026:

1. $2,500 of trips from December 2025 were paid in January 2026. They are on your 2026 form.
2. $3,100 of December 2026 trips are paid in January 2027. They go on your 2027 form.
3. In June 2026 the state took back $900 for an old overpayment by holding it out of a later payment.

Before the recoupment, the payments dated in 2026 add up to $51,400, not $52,000. What happens to the $900 depends on the payer:

• Indiana reports net earnings. That is the net payment plus manual payouts, minus refunds and voids, so offsets and voids lower the total (IHCP module, March 2025). In this example, a payer that nets the offset reports $50,500.
• Ohio shows the parts. Its portal’s 1099 summary (Provider Financials user guide, version 1.0) lists system earnings, manual earnings, claim refunds, non-claim refunds, the void amount, backup withholding, and net earnings, so you can see each adjustment.
• Some payers report the gross amount. IRS rules say to report the amount that counts as your income, which is often the gross before money you owed was taken out (26 CFR 1.6041-1(f)). CMS told Medicare contractors to report the full $1,000 when they paid $700 and kept $300 toward a prior-year overpayment (Transmittal 498, May 29, 2009). A payer that reports this way shows $51,400.

Two more items can sit on the form even though you never got the cash. Indiana’s 1099 includes payments it sent to a lien holder on your behalf, and any backup withholding it sent to the IRS. If a recovery is still open, see Medicaid recoupment.

How to check your 1099 against your records

1. Get every form. In Ohio, a portal administrator, or an agent given the “1099 Information” role, opens Provider Financial Self Services, picks the 1099 activity type and the year. As of June 30, 2024, Ohio’s portal holds 1099s from 2023 on. For older years, call the Integrated Help Desk at 1-800-686-1516, option 1, then option 5.
2. Total your deposits by payment date from January 1 to December 31 for each payer, using each remittance advice. The NEMT payment log keeps this in one place, and how to read a remittance advice explains each line.
3. List the differences. Mark payments that crossed the year line, recoupments, voids, liens, and withholding.
4. Check the name and tax ID against your W-9 and IRS records.
5. Report all your income. The IRS tells sole owners who file Schedule C to report business income from all sources, and to check their 1099s against it (Schedule C instructions, 2025). A lost or missing form changes nothing.
6. Keep the proof. Pennsylvania tells providers to keep remittance advices for at least four years. For your other records, see NEMT bookkeeping.

What to do when a Medicaid 1099 is wrong

Ask the payer for a corrected form, in writing. Each payer sets its own process:

• Indiana. Send a copy of the 1099 and your proof to Gainwell, Finance Unit, 1099 Processing, PO Box 50458, Indianapolis, IN 46250-0418. It must arrive by March 1 for a corrected form to be issued.
• Pennsylvania. Write to the Department of Human Services, Office of Medical Assistance Programs, Division of Operations, Attention: 1099 Unit, P.O. Box 8050, Harrisburg, PA 17105. It corrects a form when the tax ID does not match the name, or when the amount does not match claims processed that year. For payments made under the wrong provider number, you adjust the claims and refund the money, and that must be done before the year closes to change that year’s form.
• South Carolina. Call the Provider Service Center at 888-289-0709, the number in the state’s provider manual of July 1, 2026.

Answer a B notice right away. When the name and tax ID on a payer’s 1099 do not match IRS records, the IRS sends the payer a CP2100 or CP2100A notice. The payer then has 15 business days to send you a first “B” notice with a blank W-9 (Publication 1281, December 2023). Return the signed W-9. If you do not, the payer must start backup withholding of 24 percent of your payments within 30 business days of the IRS notice it received. A second B notice within three years needs a copy of your Social Security card, or IRS Letter 147C for an EIN.

In Indiana, the IRS checks the names and tax IDs Gainwell reports twice a year, in spring and fall. Withholding shows on your remittance under “Payments to Lien Holders” as Withholding, and Gainwell cannot refund money it already sent to the IRS. You claim the amount withheld as a credit on your tax return. For the rest of your tax year, see NEMT business taxes.