The IT agency's director of service implementation Richard Jeavons told the conference that the IT strategy was simply being 'refreshed'.
A spokesman for Connecting for Health said this was to bring NHS IT policy in line with ongoing health reforms.
'This is not a root-and-branch review of Connecting for Health,' he said.
GPC negotiator Dr Richard Vautrey said that the review of priorities over the course of a 10-year IT plan was vital.
'You can't set strategy and expect IT and people's expectations not to change along the way,' he said. 'Now is an appropriate time to check everything is as it should be.'