A local health group has raised concerns about the clinical advice given for breast cancer drug Herceptin.
The PCT said Herceptin may not be effective for all patients
Newbury and Community Primary Care Trust lodged an appeal against the National Institute for health and Clinical Excellence's draft guidance.
In June, NICE gave its initial backing for the NHS to use Herceptin.
But the Berkshire PCT said the drug watchdog's guidelines were not clear about patient treatment, cost effectiveness and potential risks.
Bruce Laurie, chairman of Newbury and Community PCT, said: "Whilst welcoming the draft guidance, the appeal is designed to clarify the practical implementation of the ruling for the benefit of patients and the population we serve."
The appeal was heard on Wednesday.
NICE's appeal panel will now have 20 working days to report back to its guidance executive.
Should the appeal by upheld, there is the possibility that a new consultation for the drug will be submitted. If it is not, NICE will issue its final guidance for the NHS in the coming months.
Herceptin, also known as trastuzumab, works by targeting the HER2 protein, which can fuel growth of breast tumours in women with HER2 positive breast cancer.
This kind of cancer accounts for about 20% of all breast cancer cases
The NICE draft guidelines recommend that all women with early-stage HER2 positive breast cancer who have completed standard therapy, such as chemotherapy or surgery, should be treated with the drug for 12 months.
But the PCT said the guidance did not take into account clinical trial data that suggested some women may respond better to the drug than others.
It also highlighted studies which revealed a shorter period of treatment than the 12 months recommended could be just as effective.
The PCT added that NICE's assumption that all women had the same capacity to respond to a year's worth of treatment meant the cost effectiveness for the NHS might not be as attractive as initially presented.
Newbury and Community PCT also drew attention to the fact that the longer term risks and benefits for the drug were still unknown.
The main serious side-effect of the drug, weakening of the heart muscle, had not been properly investigated, it said.