The centre in Telford opened to patients in September.
Parent Alison Davies-Friend said the sewage came down the walls of the children's ward two weeks ago.
Shrewsbury and Telford Hospital NHS Trust said there had been issues with leaking pipes in the women's services ward, above the children's ward.
Debbie Kadum, chief operating officer, said: "This has not impacted on patient safety.
"However, we recognise that at times, some people have noticed a smell as a result of leaks.
"We are aware of the issues and we and our contractors Balfour Beatty are working hard to resolve them."
The centre, which relocated from Shrewsbury, is the main base for children requiring an overnight stay, ongoing cancer treatment and haematology care.
But other parents have also said there have been treatment delays since it opened and say it does not cater for families, there are no toys for the children or wi-fi-connection.
Heather Noden, from Market Drayton in Shropshire, said her nine-year-old daughter, Molly, had to wait two days for a blood test compared to waiting just 15 minutes at the previous centre in Shrewsbury.
Lynne Evans, from Llangadfan, said: "There's nothing for them to do toy-wise, craft-wise, computer-wise, nothing that my daughter relied on to give her some of her life back.
"I came away very upset for children who are fighting for their lives now."
The trust said it takes time to learn how best to provide a service in a new environment, but it was already seeing big improvements in response times for blood tests and it was confident these would continue. to improve.
The spokesman said the first priority had been to ensure the safe transfer of clinical services.
"Now that we have moved into the new unit we all have an opportunity to understand what it feels like to work there and to receive care.
"This gives us an opportunity over the next few weeks to work with patients and families to design a great environment of care.
"This includes choosing the images for the walls, agreeing on the right toys and equipment and installing wi-fi for patients and their families."
Parents of children being treated at a new £28m women and children's centre say sewage leaked on to a ward.