Yula Williams, 30, said she could hear her eight-month-old baby Xavier "screaming and crying".

"It made me terrified to know that my son was inside the centre, locked and in the dark," she said.

Ms Williams had dropped her son off at the centre in the Darwin suburb of Wagaman around 8am (CST) on Tuesday and went to work.

She had dropped her car off at a local mechanics and arranged for one of her cousins to collect her son from the centre before it closed at 6pm (CST).

But when she arrived home later that night her son was not at the house.

"It was just a mother's instinct that I went back to the childcare centre and looked around," she said.

Ms Williams arrived at the centre shortly before 6pm but staff had already left the building.

After scanning all the the security screens the frantic mother climbed the back of the building to call Xavier's name through elevated slats.

"I couldn't hear him from the outside but when I walked around and called through the vents to the bedrooms I heard him scream," she told ABC radio in Darwin.

Desperate to get to her tiny son, Ms Williams then picked up a brick from the garden bed and smashed it through a window.

Police arrived at the scene about 7.30pm (CST) after they were called by one of the mother's relatives, who told them a baby was missing.

St John Ambulance officers also attended the centre to ensure the child was in good health.

They left soon after giving Xavier the all clear.

Ms Williams said that while she could understand the misunderstanding with her relative over the pick-up arrangements, she could not understand how the centre had not called her to let her know that no-one had come to collect her son.

"I didn't receive a telephone call at all," she said.

Police said they were continuing to conduct investigations into the incident.