A NICE cost impact analysis shows the indicator - for physical activity advice in patients with hypertension - will increase each practice's workload by up to 15 hours a year.
Practices will be paid just £470 on average to hit the target - less than what NICE predicts it will cost in GP and nurse time.
Doubts have also emerged over whether the target will be clinically effective, after evidence showed regular follow-ups are needed for patients to see a benefit. The QOF target only encourages checks once per year.
The GPC said the measures 'simply won't be cost effective for practices to do'.
'Not cost effective'
Almost all of NICE's proposed indicators will be added to the QOF from April following the settlement over the 2013/14 GP contract, including two new hypertension indicators.
These will award practices up to three QOF points to offer the General Practice Physical Activity Questionnaire (GPPAQ) each year to the 7.3m patients with hypertension in England. A further three points are available if they provide brief advice to those deemed 'less than active'.
Pilots in 2011 found as many as half of all patients would need a brief intervention, most often delivered as a 1-2 minute discussion at the end of a consultation.
This would lead to an extra 121,667 hours of consultations by GPs and nurses each year across England. For an individual surgery, it is the equivalent of a GP working an extra two days a year just to maintain income.
Longer consultations may be needed, as evidence suggests only 25-50% of these interventions can be delivered opportunistically.
NICE estimates it will cost £5.7m a year in GP and nurse time to offer checks to 90% of eligible patients - the upper threshold required for maximum points.
Yet, if all practices earned the full three points, the QOF money allocated would be just £3.8m.
In its formal response to the DH consultation on the GP contract, GP leaders had warned the targets would force GPs to offer longer consultations and may drain resources from other services.
GPs in Scotland and Wales will not face the indicators after they were scrapped during negotiations. The Northern Ireland government is due to confirm QOF plans soon.
GPC deputy chairman Dr Richard Vautrey told GP: 'We believe GPs already ask and advise patients about exercise when it is clinically appropriate to do so but forcing GPs to use a specific tick-box survey undermines GPs' professionalism.
'It simply won't be cost effective for practices to do this as the resource that could be achieved through QOF won't pay for the clinical time spent completing the survey. Through the government's imposition, QOF points have been spread too thinly and we expect practices to take a much closer look at whether it is sensible to chase every point in the future.'
Follow-up 'needed for long-term benefit'
The QOF already pays GPs to offer advice on physical activity but only to patients with a diagnosis of hypertension after 2009.
Evidence considered by NICE in 2006 found some evidence in favour of brief intervention. But it also found that 'for the effect to be sustained at one year, the evidence suggests that several follow-up sessions over a period of 3-6 months are required after the initial consultation episode'.
It means that a single brief intervention as incentivised in the new QOF indicator may not be enough by itself to gain the health benefits as described in these studies.
NICE's analysis of the indicator pilots also found that referral to exercise classes, required as the next step after brief intervention in some cases, was often unavailable.