The company said productivity levels at its warehouse, operated by logistics provider Tibbett and Britten, have been below those planned, resulting in "product availability issues".
Because of the lower stock levels Mothercare has suffered a fall in like-for-like sales for the past three weeks and it expects figures to remain down for the next few weeks, a company spokeswoman said.
She insisted that the stock management system itself was working, but that "the application of the system to the warehouse processes" was at fault.
The spokeswoman admitted that this could be caused by a lack of properly trained staff at the site in Daventry, Northamptonshire.
To overcome the problems Mothercare has asked some of its major suppliers to deliver directly to its outlets and is also using another warehouse to improve the flow of stock to stores.
The spokeswoman said Mothercare hoped that the problems would not affect the vital Christmas trading period.
"Tibbett and Britten said the system will be functioning properly within weeks rather than months," she said.
A Tibbett and Britten spokesman said, "Lower-than-planned productivity levels in the warehouse resulted in a very rapid build up of stock and consequential site congestion. This led to the recent difficulties, while additional resources were brought into play."