Isner was trailing Martin Klizan of Slovakia 6-2 7-6 in the first round of the Australian Open on Tuesday before retiring because of an ankle injury he first suffered at the Hopman Cup earlier this month.
The American, who missed the Melbourne tournament last year because of a knee injury, won the title last week in Auckland but felt more pain in practice on Tuesday and was not sure if he would be able to complete his match.
By playing, Isner guaranteed himself at least the first-round loser's prize money of A$30,000 ($27,200).
Had he pulled out before the match a lucky loser from the qualifying event would have been promoted into the main draw.
"I think in a situation like that, maybe a rule could be put in place where the person who pulls out gets compensated 75 percent, 80 percent, maybe even 100 percent of the first round prize money," Isner told reporters.
Slovenian Polona Hercog prompted criticism earlier on Tuesday when she retired after one game of her women's singles match against Alize Cornet of France.
Hercog also collected A$30,000 for her 10 minutes of first round action.
"I would be in favour of a rule change because (Hercog) earned her spot in the main draw and if she's hurt, you don't want to go out there and play one game," Isner said.
"But I think she deserves to be compensated in some way and have a lucky loser come in and play for second-round prize money and points.
"At this point I would think the lucky loser is just happy to get in."
The American said he was confident he would be fit to take his place in Jim Courier's U.S. Davis Cup team for the home tie with Britain which begins in California on January31.
"I have two-and-a-half weeks, I believe I can make it," he said.
"That's my goal, to be 100 percent fit, not 95 percent, because Courier's not going to put me out there if I am not 100 percent."
Isner's defeat leaves world number 51 Sam Querrey as the highest ranked American remaining in the draw. ($1 = 1.1043 Australian dollars)
(Editing by Patrick Johnston)
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