Around a dozen teenagers were in the centre when the alarm was raised on Tuesday night.
A bomb warning was telephoned through at around 5.20pm and staff told UTV that Óglaigh na hÉireann that claimed responsibility.
"My understanding is they said it was from Óglaigh na hÉireann and that there was a bomb in the back yard," said Geraldine O'Kane from the centre.
"I don't think there's any justification for what they did. I don't understand why they did it."
The Greater Whitewell Community Survey is a cross community project supported by both the Stormont Executive and the International Fund for Ireland.
It lists its aim and objective as providing a better quality of life for all in the Greater Greencastle and Whitewell community.
Project organisers are therefore shocked that their building has been targeted.
"For a start, we work for this community," continued Ms O'Kane.
"We work for all this community to make this a far better community for everybody. We try our best to get a shared space for all the young people to come together and for everybody to come together. So we're a wee bit shocked as why?"
Army bomb experts found a viable pipe bomb when they were called to the centre.
It and a number of other nearby homes and businesses were evacuated for a time, and disruption was also caused to traffic.
The attack has been condemned by politicians, who said that despite enduring its share of sectarian hatred, the Whitewell area had consigned such scenes to the past.
Sinn Féin Councillor Tierna Cunningham said: "Why anyone would want to target the Greater Whitewell Community Surgery is beyond belief.
"The community centre was obviously affected and local residents had to leave their homes while the device was dealt with. No doubt whoever was behind this will not be stepping forward to explain their actions as they know the community is disgusted with it."
Nigel Dodds, North Belfast DUP MP, said: "This has caused a great deal of shock within the wider community and I encourage community workers in the area not to be deterred from the positive work they have been engaging in.
"Community Workers from Whitewell, White City, Fairyknowe and Graymount all meet in the surgery alongside young people from each area."
Anyone with information on the incident can pass it on to the PSNI.