Dr Brian Keighley’s comments come after the Scottish government claimed that all 14 health boards would see a real-terms boost of 2.9% in their budgets next year as they split £8.8bn between them.
But Dr Keighley claims the impact of inflation in the cost of healthcare which currently stands at 4%, would mean cuts would still have to be made.
He said: 'Despite the budget announcement made by the cabinet secretary, there is no denying that the NHS faces an unprecedented real-terms reduction in its budgets for the first time since devolution. It would be naïve to expect that this will not have an impact on patient care and access to healthcare services.
'It is important that in responding to the challenges set out in this budget, that politicians look to the dedicated professionals working across the public sector to help them to make the changes and achieve the savings required without compromising on service or care provided to the public.
'It is disappointing that cuts to the NHS workforce and attacks on doctors’ contracts and pensions have been identified by some as the way to navigate through these difficult financial times. While this might deliver some savings in the short term, this approach will have a long term and persistent damaging impact on morale and patient care.'
The government also claims funding for 2013-14 looks set to rise by 3.3% in 2013-14 and by 3.1% in 2014-15.
Health secretary Nicola Sturgeon said: 'The Scottish government is committed to protecting spending on health, and this budget allocation reflects an increase in real terms for every territorial health board across Scotland.
'Despite a difficult economic climate, we know how important it is that we continue to invest in frontline NHS services, and that is why the core budgets of all territorial health boards are increasing in real terms.
'Sustained investment in our national health service will ensure that boards continue to have the necessary resources to bring about real benefits to both patients and staff, and that we can deliver a first class service to patients across the country.
'This funding will help us continue to provide more sustainable, high quality and improving healthcare services. It will also support the integration of prison healthcare into the NHS, enable the Scottish Ambulance Service to implement the meal break settlement, and it will help us deliver the 18-week referral to treatment waiting times standard.'