Martin sued the tour and won the right to use a golf cart in February. The PGA appealed, claiming it is not covered by some ADA rules and that using a cart removed the element of fatigue from the game.
Martin suffers from a congenital malformation of the blood vessels in one leg, causing severe swelling, pain and difficulty walking. The problem, diagnosed when the 25-year-old golfer was a child, worsened to the point that he can no longer walk 18-holes, Martin argued in the federal discrimination suit filed last year.
The Justice Department's ability to enforce the ADA could be threatened if the PGA Tour wins its appeal, the department's friend-of-the-court brief said.
"Walking has nothing to do with the skill it takes to execute golf shots during a competitive golf tournament," acting Assistant Attorney General for civil rights Bill Lann Lee wrote.
PGA spokesman Bob Combs said the organization's position is unchanged.
"We've continued to welcome him as one of our competitors and members," Combs said.
Martin has played in two top-level PGA Tour events this year and several of the less-competitive Nike Tour events, Combs said. Martin also qualified for the U.S. Open, which is not a PGA event.
The federal appeals court has not said when it will hear the case.
At issue is whether PGA tournament courses are public areas under the disability rights law and whether modifying PGA rules would fundamentally alter the game.
The PGA argued that the greens and fairways are not open to the public during a tournament and thus do not have to be accessible to the disabled.
"The mere fact that access is strictly controlled does not mean that a facility is not a place of public accommodation," the Justice Department wrote.
On the second point, the Justice Department noted that some PGA events allow carts, and argued that carts in and of themselves do not change golf competition.
Furthermore, Martin's disability is so debilitating that he doubtless is more tired even using a cart than able-bodied golfers who walk, the Justice Department said.
The brief, filed with the 9th U.S. Circuit Court of Appeals in San Francisco, does not mean the federal government will take Martin's case and the appeals judges are under no obligation to heed the department's arguments.
The Justice Department did not weigh in on the case in the lower court.