The sport's ruling body said on Thursday that Lenton's time of 52.99 seconds, which she posted as lead-off swimmer in a mixed 4x100 freestyle relay between Australia and the United States in Sydney three weeks ago, would not be officially recognised.
Lenton's time was 0.31 seconds under the world record set by German Britta Steffen at last year's European championships in Budapest.
"It is an unfortunate situation and our hearts go out to Libby because it was truly an amazing performance from an amazing young Australian swimmer who I'm sure will continue to aspire to lower the world mark," Swimming Australia chief executive Glenn Tasker told reporters.
Lenton, who won the 100m freestyle and four other gold medals at this year's world championships in Melbourne, has twice previously held the world record.
