The institute has identified 19 guidelines which if fully implemented could save PCTs up to £800m.
But delegates at the annual NICE conference in Manchester last week warned that many PCTs lack the budget to follow its guidance.
NHS Alliance GMS contract lead Dr David Jenner said it cost PCTs too much up front to follow NICE advice, and savings were slow to appear.
‘The NICE CKD guidance has increased the number of patients being referred for kidney testing,' he said. ‘PCTs are having to employ specialist nurses to meet the guidance.
'As for the depression guidance, my PCT has given up on working out how it can afford it. It recommends 16 sessions of cognitive behavioural therapy (CBT) but many PCTs do not even fund CBT.'
NICE should say what parts of its guidance should be implemented first so PCTs can prioritise, said Dr Jenner.
Jenny Field, associate director of commissioning at NICE, insisted that following its advice could cut costs.
She said advice on long-acting reversible contraceptives could save huge sums by cutting unwanted pregnancies.
There are also savings to be made by following NICE public health guidance, by cutting obesity and smoking, although it is very difficult to quantify, said Ms Field.