Building rubble left in drains in Canberra Hospital's new critical services building has caused blocked toilets and an overflow of waste.
The hospital's builder, Multiplex, was called in to implement urgent fixes to the pipes.
An ACT government spokesman said the issues had affected some inpatient spaces, clinical areas and family rooms.
"There have been instances of toilets blocking up and waste overflowing in the new building," the spokesman said.
"Investigations of the issues have identified a number of factors. This includes blockages from paper towels being flushed down toilets and other items including wet wipes, hair nets and booties also causing blockages.
"The first instance was related to building rubble in the drain system, which was obviously very disappointing.
"Following notification of the issues, Multiplex was on-site quickly and commenced investigations and rectification work."
The new critical services building at the hospital was opened on Saturday, August 17 and health authorities moved the bulk of the services on the day.
The new building has the hospital's emergency department, the intensive care unit and operating theatres.