Athletes are required to file information on their whereabouts every day to allow drug testers to locate them for random out-of-competition tests.
Fraser-Holmes, who won a 200 metres freestyle relay bronze at the 2015 world championships, had fallen foul of the 'whereabouts' rule and missed three tests, local media reported, citing the swimmer's lawyer.
Swimming Australia confirmed world governing body FINA had banned the 25-year-old after a hearing.
"We have been informed that Thomas Fraser-Holmes will be appealing the decision to the Court of Arbitration for Sport, as is his right," SA said in a statement on Friday.
Fraser-Holmes's lawyer Tim Fuller said a problem with the World Anti-Doping Agency's software had prevented the swimmer from logging his whereabouts.
"It's a really, really strict interpretation of negligence and we feel that the doping tribunal has erred and that's why we will be appealing to the CAS," the Gold Coast Bulletin quoted Fuller as saying.
If upheld, the ban would see Fraser-Holmes miss next year's Commonwealth Games in his Gold Coast base in southern Queensland state.
Fraser-Holmes is the reigning Commonwealth Games 200m freestyle champion and won a second 200m relay gold at the 2014 Glasgow Games.
Breaches of the whereabouts rule have snared a number of prominent athletes in recent months, including American Olympic 100 metres hurdles champion Brianna Rollins and West Indies cricketer Andre Russell.
(Reporting by Ian Ransom; Editing by Sudipto Ganguly)
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