A Northern Territory Police investigation into the alleged rape of a toddler, which drew national attention to Tennant Creek, has many similarities to a "botched" homicide investigation, the ABC has learned.

Key points: Police "mistakes" led to man spending three months in prison before charges were dropped

Police "mistakes" led to man spending three months in prison before charges were dropped Police accused of failing to set up crime scenes, gather and test forensic material, check witness statements and alibis

Police accused of failing to set up crime scenes, gather and test forensic material, check witness statements and alibis Allegations of mistakes similar to that of "botched" investigation in the death of Sacha Green

Alleged police mistakes led to a man spending three months in prison after being accused of raping a two-year-old girl in the remote town, 450 kilometres north of Alice Springs, before the charges against him were dropped in June.

Another man has since been charged over the February crime, and is due to appear in court this month.

The first man told the ABC that he was in hospital at the time of the alleged rape, but said police did not seek to verify that alibi.

Two other separate sources alleged to the ABC that police failed to secure a crime scene, and that they relied heavily on accounts that they then failed to verify.

They also said there was a delay in getting forensic evidence tested.

Sources, on condition of anonymity, told the ABC that semen found on a nappy did not match the DNA profile of the first man they arrested.

"For a crime that got such attention, you have to wonder why senior police weren't looking over their shoulder, making sure everything was kosher," a source said.

The ABC sent NT Police a list of questions, including how long the first man was kept on remand after the DNA evidence suggested he was not responsible.

"Northern Territory Police are unable to comment as there is an ongoing investigation and the matter is currently before the courts," a police spokesperson responded.

Case comes after coroner looked at 'botched' probe

The alleged rape occurred after police had already faced difficult questions about their competency at a coronial hearing into the suspicious death of Indigenous woman Sacha Green in 2013.

NT coroner Greg Cavanagh, in his findings handed down in June, described that investigation as "botched" and led by "inexperienced and incompetent" police.

The allegations of errors in the toddler rape case are similar to the mistakes made in the Green case, including police not establishing secure crime scenes, not sending off forensic material for testing and taking too long to verify witness statements.

NT Police were slammed in the coroner's report on the Green case, which cited similar mistakes made while investigating the suspicious 2007 death of an Indigenous boy in Borroloola (who cannot be named for cultural reasons) after which police promised to learn from and to improve their investigations.

No-one was ever charged over either the Borroloola boy's death or over Ms Green's death.

"What is it about Tennant Creek that these same mistakes keep getting made? Why aren't senior police getting involved?" said one source.

The fallout from the alleged child rape continues, with federal cabinet ministers Nigel Scullion and Dan Tehan touring the town this week on orders from Prime Minister Malcolm Turnbull, who had been criticised for not visiting the town or committing more funding to tackle social dysfunction in remote communities.

There has also been ongoing debate about what sort of restrictions, if any, should be imposed on alcohol sales on the town and the broader Barkly region of the NT.