Health and Social Care Minister Howard Quayle says he understands the disappointment felt by the Children's Centre.
There's been an outcry over the decision to award child care contracts to another provider. Some 38 Children's Centre staff are likely to be affected by the changes.
St Christopher's will take over residential services from next month.
Mr Quayle said: 'The primary principle for the department in awarding contracts is to secure services that are of the highest quality for the children we care for, and which offer good value for the public’s money. On this basis St Christopher’s were evaluated as the strongest bid.
'The department understands the disappointment felt by the Children’s Centre, which as a result of this competitive process will now cease to provide any residential service for us. In line with the procurement process we have now given written feedback to them on their unsuccessful bid.'
He said the Children's Centre continued to hold government contracts worth a total of ?2.2million a year.
Backbench MHKS are now lobbying the government over the contracts and public petitions have been set up.
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