Scotland's spending watchdog has expressed concern about Edinburgh's planned airport rail link.
It is unlikely to be up and running by the 2011 target date, according to Auditor General Robert Black.
However, he gave a second project, to deliver trams for the Scottish capital, a clean bill of health.
Finance Secretary John Swinney, who has expressed concerns that both projects do not represent value for money, said the findings had raised serious issues.
The Scottish government's decision to call in the auditor was heavily criticised by Labour and the Liberal Democrats, who said his report gave no reason to scrap the two schemes.
Although both the trams and airport projects previously received parliamentary backing, no decision has been taken over their future.
The auditor general's report stated that the estimated £593m cost of the trams project had been subjected to "robust testing" and sound financial management.
However, as well as concerns about delivery of the airport rail link, which may cost up to £650m, the auditor said there was a higher level of uncertainty over the project than might be expected because "key decisions" had yet to be made.
Mr Swinney claimed he had been vindicated in his decision to order the investigation, adding that it had provided further information on which a decision could be made.
"The report raises a number of serious concerns about governance and development issues which we would have expected to be in better shape than the auditor general finds them, particularly in relation to the Edinburgh Airport rail link," he said.
Former transport minister Tavish Scott said the project should go ahead without delay.
"The government doesn't have any evidence from this report to cancel these projects and must commit to funding immediately," added the Lib Dem finance spokesman.
Green MSP Robin Harper said the trams were a good deal for the taxpayer and the environment, but added: "The airport rail link is the wrong option, poor value for money and is not environmentally sustainable."
Tory transport spokesman Alex Johnstone said the airport rail project so far seemed to have been a "shambles", adding: "It is too early to make a judgement about the budget, but I am deeply concerned at the criticism of the running of the scheme to date."
The government was urged to proceed with the trams project
Des McNulty, the Labour transport spokesman, said the biggest risk to the trams project was "continued procrastination" by the government, while he claimed that scrapping the airport rail link would put in doubt other public transport projects.
"The report has identified a number of management issues, the most crucial of which are to do with the management and financing of risk and the commitment of key stakeholders," he said.
"It is the responsibility of ministers to ensure that these are resolved, in order that the project can be taken forward."
Tie, the organisation managing the two projects, said it shared the auditor general's concerns over the airport link and was working to resolve them.
Executive chairman Willie Gallagher said: "We believe it is critical to the success of the rail project that this problem is addressed without delay."