The regular meeting scheduled for December was cancelled just weeks after the GPC voiced concern at a change that makes it harder for GPs to propose new indicators.
The move marks the start of a shift towards NICE using its own quality standards and guidelines, rather than stakeholder views, to develop new QOF targets.
NICE denied the cancellation would set back the QOF and insisted the process was still 'open and transparent'.
It comes after the institute withdrew the established system for proposing new QOF indicators in October.
At the time, experts warned the changes may marginalise rare conditions and limit public and charity input.
The GPC said it would be 'extremely concerned' if contributing ideas to the QOF was more difficult.
The cancelled meeting usually takes place twice a year and decides which indicators should be put to GP negotiators for inclusion in the QOF.
In future, draft indicators will be created solely from NICE quality standards and guidelines rather than stakeholder views.
A NICE spokeswoman said: 'Each proposed draft indicator/guideline recommendation put forward for indicator development will be part of an open and transparent process.'
Meanwhile, Birmingham GP Professor Helen Lester, who leads the design of QOF indicators, said the framework had been 'world-leading' in 2004 but now must evolve.