A woman is being counselled after allegedly catching a Brisbane childcare worker trying to rape her friend's two-year-old son.

The woman couldn't find the boy when she arrived to pick him up at the centre in Durack in Brisbane's west on Friday afternoon, so she started to search the premises.

'In one of back rooms of the child care centre, she was confronted with a 20-year-old employee ... committing a sexual assault on the two-year-old boy,' acting Superintendent Geoff Sheldon told reporters on Monday.

Supt Sheldon said the woman grabbed the child, told his mother and went straight to police.

The man was charged with attempted rape and other offences.

He was also later charged with possessing child exploitation material after police found anime files of children on his home computer.

Supt Sheldon said government support agencies were working with the boy's family and the friend who witnessed the alleged assault.

'I can't imagine anything worse, as a parent myself,' he said.

'It's a horrible breach of trust.'

But Supt Sheldon implored parents to keep their faith in the state's child protection system, describing the incident as extremely rare.

'There's free and flowing information between government departments so that anything suspicious gets looked at in a timely fashion and thoroughly investigated,' he said.

Supt Sheldon said it was hard to tell if the boy could comprehend what had happened to him.

The childcare worker had been at the day care centre for about six months and hadn't held any previous jobs, he said.

The man was released on bail on Saturday morning to reappear in Brisbane Magistrates Court on October 12.

He is also required to appear in Richlands Magistrates Court on Friday on the child exploitation charges.

AAP