The papers were presented to a meeting of health board chief executives and civil servants last month.
They suggest the NHS is facing a £400m funding gap, and sweeping changes will be needed for boards to break even.
The Scottish government said it was committed to "protecting and increasing the NHS budget".
The papers were passed to the BBC and The Herald by a senior NHS whistleblower, who said they had become frustrated by the argument of the "Yes" campaign that the biggest threat to the NHS comes from the UK government.
The documents state: "The status quo and preservation of existing models of care are no longer an option given the pressing challenges we face."
The whistleblower has alleged that pressures on the NHS come from Scottish government policies.
The confidential documents relate to a meeting held by NHS bosses on 6 August 2014.
As part of an initiative to transform care by 2020, legislation has been passed by the Scottish government to encourage more community care.
However, the papers say this has been undermined by "continued commitments" which are "directly in conflict" with the 2020 vision and increase the cost of expensive hospital care.
The documents say new obligations are "not fully funded".  The documents conclude that the "status quo in terms of service and workforce planning is not an option".
The papers outline a funding gap of £400-£450m in the next two financial years, 2015-17, which is described as "a level significantly in excess of that previously required".
The documents suggest that health boards will have to consider centralising hospitals and closing services - a measure which the SNP vowed to stop when it was elected in 2007.
The Scottish government reversed the closure of Accident and Emergency departments at Monklands and Ayr hospitals, but the papers suggest such dramatic measures may be back on the table.
"Radical and urgent decisions need to be made regarding the shape and configuration of services," the document states.
But it also points out that boards are "without the mandate and authority to implement the scale of change and redesign required".
"We need to commit to these priorities and accept that significant changes require to be implemented," the papers conclude.
The whistleblower told the BBC: "Services are unsustainable right across Scotland from three emergency centres in Lanarkshire, to emergency care at the Vale (of Leven) to paediatrics at St John's (in Livingston), and with particular issues for more rural boards, hence the problems at Grampian.
"The current pattern of services is underpinned but short-term money and fixes won't stack up going into next year.
"There is a complete gap between policy announcements about care in the community and more money for primary care, and the announcements and commitments which continually increase the cost of acute care."
The Scottish government said the paper was "part of the regular discussions among NHS leaders to plan for NHS Scotland's future".
Health Secretary Alex Neil said: "We've protected Scotland's NHS from the Tories' cuts, and with independence we can ensure that it is never again under threat from Westminster's dangerous obsession with austerity.
"Despite Scotland's budget being slashed by 7.2% by George Osborne between 2010/11 and 2015/16, our increases in health spending means that the NHS is receiving record high funding, with a budget increase of over £1bn between 2010/11 and 2015/16."
He added: "To ensure we can continue to develop the NHS, it's important that NHS boards regularly discuss their future plans to inform budget discussions with Scottish government officials, and to identify how we will continue to deliver quality care and treatment.
"We continue to develop our health service to meet the changing demands of the people of Scotland, and that's why we've already legislated to integrate health and social care from April next year.
"This integration of services is particularly important to ensure our elderly population is kept well and provided with care in the best setting for their wellbeing."
Confidential papers passed to the BBC suggest a radical cost-saving plan will be implemented in the Scottish NHS after the referendum.