GPC negotiator Dr David Bailey admitted it was 'possible' some of the QP indicators were not evidence-based, and flew in the face of the original, clinically-led framework.
The QP indicators, which paid GPs to cut prescribing costs and avoid referrals and hospital admissions, were added to the QOF in April 2011.
The indicators have faced criticism from the profession. Earlier this month, GP revealed how 58% of GPs responding to a survey said they had experienced 'inappropriate' pressure to cut admissions from the quality and productivity indicators introduced last year.
Just 15% of the 667 GPs surveyed believe the targets have benefited patients.
GPC senior members faced questions from LMC representatives at the LMCs conference on Wednesday.
Asked why QP indicators were introduced, GPC negotiator Dr David Bailey said it was 'pragmatic negotiating'.
He said: 'We were in a position last year where we had to negotiate a contract to maintain the value of QOF at 1000 points in the face of a government that wants to make signficiant efficiency savings.
'I completely accept they are not in the spirit of the original clinically driven QOF, and its possible that some of them may not be evidence-based.
'This, I'm afraid, was pragmatic negotiating. It's not the purity of the QOF we had in 2004, which was quite clearly to drive up the quality of patient care. But if we wanted to maintain a 1,000-point OQF, I'm afraid it was the price we had to pay.'
GPC chairman Dr Laurence Buckman said there would be no new GP contract negotiated in the near future. 'A new contract would lead to new winners and losers,' he said. 'We're better off taking what we have and remodelling it.'
He said there was little enthusiasm for a new contract in the current situation and given the government does not want to discuss one.