A 25-year-old man has been charged with manslaughter and sexual intercourse without consent over the death of a five-month-old baby in Alice Springs.

Key points: The baby had symptoms consistent with shaken baby syndrome

The baby had symptoms consistent with shaken baby syndrome A 25yo man has been charged with manslaughter, sexual intercourse without consent

A 25yo man has been charged with manslaughter, sexual intercourse without consent The mother says she had begun to lost hope an arrest would be made

Warning: This story contains distressing details about a baby's injuries.

NT Police said the child died on July 26, 2012.

The man was arrested this morning after an extensive police investigation and an inquest held in 2016 which revealed "further avenues of investigation", officers said.

An autopsy showed the baby had 26 bruises to his body, over both bones and soft tissue, and had injuries consistent with "shaken baby syndrome", including haemorrhages to both eyes and cerebral swelling.

The inquest heard the baby also had anal injuries, blood in his nappy and semen was found.

The boy had been with a carer at the time, who told police he caught the baby as he fell from a change table.

But a forensic expert told the 2016 inquest that would not have caused the fatal head injuries.

Last year the Northern Territory coroner found offences may have been committed and referred the case to police, but no-one had been charged until today.

The 25-year-old man was refused police bail and a court date is yet to be set.

Six years on, mother started to lose hope

The mother of the baby says after six years, she had lost faith in the investigation. ( ABC News: Steven Schubert )

The baby's mother, who cannot be named for legal reasons, said she had started to lose hope an arrest would be made.

"It was honestly probably the best feeling in nearly six years," she told the ABC of receiving the news about the charges.

"I was shocked, it wasn't expected. I'd started to, I guess, lose hope," she said.

"I have rung family to let them know that it does look like everything is finally going ahead."

She said after six years, she had lost faith the investigation would develop further.

"It was shock, joy, relief... I wasn't going around in circles for no reason."

"I'd lost faith in the [Director of Public Prosecutions] a long time ago because they kept pushing it backwards saying there was more [evidence] that they needed. So I always questioned would they have enough."

'I haven't broken my promise to my baby'

The mother said she thought of her baby when police told her the news of the arrest.

"[I thought about] all the good things. The fact that I haven't broken my promise to [the baby]."

She thanked police and the Director of Public Prosecutions for their efforts.

"[I'm] hoping that the truth actually comes out, that's what I want to happen next," she said.