Detective Superintendent Des Bray says 43 children have now been eliminated as potential victims.
"I can confirm that Madeleine McCann has been totally excluded as a potential victim and UK police have been advised," he said on Wednesday.
Three-year-old Madeleine went missing from her holiday apartment in Portugal in 2007.
Some overseas websites have reported on the SA discovery, speculating whether the remains belonged to the UK girl.
The bones were found earlier this month in scrub alongside the Karoonda Highway near Wynarka, east of Adelaide.
Police believe they belong to a fair-haired girl aged between two-and-a-half and four who may have been murdered up to eight years ago.
Supt Bray says a task force set up to investigate the girl's death has taken more than 500 reports through Crime Stoppers.
Suitcase murder -what we know so far
* The victim was a young girl aged between two and a-half and four.
* She was likely caucasian with fair hair about 18cm long.
* She was 90 to 95cm tall.
* She was killed at another location with her body put in a suitcase before being brought to SA.
* She was killed some time after the start of 2007.
