NT police defends investigation into alleged rape of toddler

The Northern Territory police force has defended its investigation into the alleged rape of a two-year-old.

It comes after charges were withdrawn against a 24-year-old originally accused of the alleged assault earlier this year, following fresh charges being laid against a second man on Monday.

The 25-year-old man is now on remand accused of the assault.

Acting Assistant Commissioner, Tony Fuller, spoke to 9NEWS and revealed new evidence had come to light, but wouldn't elaborate on the new information.

"The matter is still under investigation. We stand by the original arrest. The arrest was made on the evidence we had at the time and just goes to show we don't stop an investigation because someone's under arrest. We'll consider all evidence," Mr Fuller said.

He denied it was a police bungle and wouldn't rule out any future charges.

He did admit it was a possibility the man could attempt to seek compensation after being in custody for three months.

"That's up to the individual... All these investigations are complex.

"It's a complex environment. There is vulnerable witnesses involved here, there are persons involved with alcohol. It's not as simple as people think."

NT Children's Commissioner conducted an investigation after the alleged rape was revealed.

Colleen Gwynne found there was a "foreseeable risk of harm" to the two-year-old, given the family had over 150 interactions with police and they had been the subject of 52 child protection notifications.

The 25-year-old accused is scheduled to face court in late July.