Under transitional arrangements set out when the NPPF was published in March 2012, councils with local plans adopted since 2004 were told that they may continue to give "full weight" to relevant policies "even if there is a limited degree of conflict" for 12 months.
But following the 12-month transition period, which ends on 27 March 2013, decision takers must give due weight to relevant policies in existing plans "according to their degree of consistency" with the NPPF, the framework says.
A survey, carried out by Planning in partnership with the Royal Town Planning Institute (RTPI) and Planning Officers Society (POS), reveals that 46.7 per cent of councils with plans adopted since 2004 say that the documents will need revising to bring them in line with the NPPF.
Of those councils, 71.4 per cent do not believe they will be able to have a revised local plan adopted before 27 March 2013, according to the online survey of 76 local planning authority heads of planning in England.
John Hoad, head of planning at countryside lobby group the Campaign to Protect Rural England, said the NPPF transition arrangements had created a "set up to fail" system.
"It appears that the government really wants to encourage planning by appeal," he said. "It is unreasonable to expect complex plans dealing with housing land and environmental protection issues to be completed quickly in a situation of national policy confusion."
The findings come as Harborough District Council in Leicestershire announced that it is to begin work on a new local plan, despite having only adopted its core strategy in November last year.
The council said that once the NPPF transitional arrangements end, its local plan will "not be as robust a framework as it could be to help determine planning decisions as it may not reflect up to date housing needs".
Of the councils needing to revise their post-2004 plans to bring them in line with the NPPF, 52.4 per cent said they are confident that they have enough resources to get an NPPF-compliant plan in place early enough to prevent significant development on unallocated land.
But 28.6 per cent of such councils said that they were not confident that they have sufficient resources.
The Department for Communities and Local Government pointed out that £2.5 million of funding has been made available to the Planning Inspectorate and the Planning Advisory Service to help local planning authorities to make revisions to their plans, and that some revisions would only need to be minor.
A spokesman said: "Comprehensive figures from the Planning Inspectorate show that nearly 70 per cent of all local planning authorities have now published a draft plan, and nearly half have adopted plans."
The survey also reveals that the number of professional planners employed by local planning authorities in England fell by 12.6 per cent between October 2010 and October 2012. On average, this represents a reduction of 2.8 professional planners, an analysis of the figures reveals.
Nearly three-quarters of respondents to the survey said they do not expect the recent 15 per cent increase in planning application fees to increase the resources available to their planning team later this year or next year.
RTPI chief executive Trudi Elliott said: "It is disappointing that in many cases councils continue to cut staffing levels, given the widespread recognition of the importance of planning in delivering growth, sustainable development and improving the quality of life, and the government's view of the role planning can take in generating revenue."
The full survey results can be found here.