GPC chairman Dr Laurence Buckman said the SCRs used in pilot sites did not 'update in a way you might expect' meaning they contain 'inaccurate' data that could result in 'significant dangers'.
He said: 'If you have an SCR that you cannot rely on and you cannot tell how up-to-date it is ... that is something that it is very concerning.'
The GPC passed a motion last week which called for the government to fully investigate and resolve patient safety issues relating to existing SCRs.
It also carried a motion that called for the creation of any further SCRs to be halted until the government carries out a full review of the model.
However, the GPC said the motions do not represent any advice or instruction from the GPC or LMCs to GPs.
It is up to individual practices to decide whether to upload records, it said.