The organisation's latest data shows more than 300 children accessed shelter services in 2025.
Children presenting due to domestic abuse also became more common, rising 12 per cent from 2024.
"Children are not just witnessing domestic violence; they are experiencing it as victims themselves," WCS chief executive Annabelle Daniel said.
"A major factor is the increase in child protection matters which are now more common and serious among families presenting to shelters."
Larger families are waiting longer to seek help because of the difficulty of accommodating more children.
But the longer they wait to seek help, the higher the risk escalates.
WCS has also noted a 12 per cent increase in adult shelter clients that were considered at serious threat of domestic homicide, the highest level of risk that requires immediate referral and management.
The increase in the numbers of children accessing shelters highlighted the need for ongoing investment in specialist supports, Ms Daniel added.
"Families arriving at our shelters are needing to navigate more complex systems than they ever have before," she said.
"Many are facing multiple, intersecting challenges that demand urgent, tailored support."
Across all demographics, domestic abuse is the primary reason clients are presenting at shelters, ahead of housing affordability.
A landmark parliamentary inquiry examining the relationship between domestic violence and suicide has been told children and young people impacted are often invisible in current support structures.
Research shows exposure to violence can have profound and lasting impacts on children and young people, including increased risk of suicidal ideation.
Young people, particularly those in out-of-home care, should be considered an at-risk group for both family violence and suicide, youth mental health organisation Orygen said.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
1800 RESPECT (1800 737 732)
Men's Referral Service 1300 766 491
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