The new hospital for East Lothian is the latest proposal to be thrown into disarray because of the Government's decision that new buildings should be paid for not from the public purse as expected, but through private funding.
Like the new Sick Kids hospital, which is also facing significant delays because of the dispute, health chiefs are now unsure wether they will be able to secure funding.
It means thousands of patients in East Lothian will continue to be treated at the outdated Herdmanflat and Roodlands hospitals, including the mentally ill and elderly, for years to come.
Other more long-term projects, like a new psychiatric hospital on the Royal Edinburgh site in Morningside, are also shrouded in uncertainty.
Only those which have been "legally committed" are watertight with public money safely in place. That includes the Musselburgh Primary Care Centre, the new Royal Victoria Hospital at the Western General and the refurbished Chalmers Hospital, which will host a one-stop sexual health centre.
Ministers previously endorsed public funding for projects like the Sick Kids and East Lothian hospitals, but after last week's budget announcement it emerged NHS Lothian would have to source private funding through the much-criticised Scottish Futures Trust (SFT).
The Scottish Government maintains the SFT will help spread the risk and guarantee the flow of money to make the projects possible.
One senior health source said: "There is a lot of concern over this. It is not just about these inevitable delays, but the knock-on costs of running things we know are on limited time.
"The delays cost the Lothians and people in the Lothians."
What grates even more with NHS Lothian's top management is the fact the new 840 million Southern General in Glasgow, which will contain a paediatric hospital, will be built entirely from the public purse. They see it as extremely unfair that all their major projects, past and present, including the 1.26 billion ERI, have had to be constructed under some form of private finance initiative.
NHS Lothian executives feel they are pouring money into the hands of the private sector by renting the Consort-built hospital at Little France.
The Evening News revealed last week that it will be the summer of 2015 at the earliest before the new Sick Kids at Little France is opened, two-and-a-half years behind schedule.
It has now emerged that the new East Lothian facility, which will take on services offered in Herdmanflat and Roodlands hospitals, allowing them to close, is on a similar time plan, despite the intention for it to be already open.
Susan Goldsmith, NHS Lothian's director of finance, outlined the grim warnings at a health board meeting this week.
She told senior management: "The financial position is one of concern. A system of funding will be found for legally committed projects.
"What we need to be clear about is until a scheme is legally committed there is no guarantee of cash flow."
Staff at the Royal Edinburgh are also worried about the plans to redevelop the sprawling but outdated Morningside site.
With money drying up and other major projects now overlapping its time frame, sources said they would be "surprised if it goes ahead on time, if at all".
The Scottish Government said it remains committed to the major schemes.
Lothians SNP MSP Dr Ian McKee, a former city GP, said: "I'm delighted that NHS Lothian has received an increase of 31.9m which will go towards improving patient services.
"The budget has also protected vital infrastructure projects including the Royal Victoria Hospital, the Royal Sick Children's Hospital and the Department of Clinical Neurosciences. These projects are absolutely essential."
New Royal Victoria
Construction of the elderly people's hospital at the Western General is under way. It is hoped the 50 million facility will be open by May 2012.
The refurbished building in Lauriston is more or less complete, and will house the country's first one-stop sexual health clinic, at the cost of 9 million.
Musselburgh Primary Care Centre
The 20 million facility has been delayed by the discovery of extensive Roman remains, but should be complete by the spring of 2012.
Midlothian Community Hospital
A rarity for a public sector project - it actually opened early. It has now been running for two months and is receiving rave reviews from staff and patients. Cost 18 million.
New Sick Kids
Coming in at an estimated 250 million, this is NHS Lothian's current flagship project. Health chiefs are determined it will go ahead, but timescales are slipping back, and now the health board doesn't even know how it will pay for the facility. The summer of 2015 has been pencilled in as the absolute earliest.
East Lothian Community Hospital
Talks to open the centre in Haddington began in 2005, but it will now be at least 2015 before it begins operating. Again, NHS Lothian doesn't know where the money will come from, despite being advised before it would be publicly funded.
Department of Clinical Neurosciences (DCN)
This 50 million plan has been dealt several blows in the last year. Health chiefs already knew Holyrood wouldn't pay for it, even though the reverse had been suggested to them by ministers. Problems with the Sick Kids push the brain unit even further back.
Royal Edinburgh Hospital reprovision
The gradual rebuild of the mental hospital is due to be finished by 2015, but sources have expressed fears that this too could be jeopardised as cash dries up.