The executive suffered its first Holyrood defeat yesterday and was forced to go ahead with the Edinburgh tram scheme against the will of ministers.

Alex Salmond's administration faced the threat of a motion of no confidence if it refused to recognise the will of parliament but after an 81 to 47 vote, his Finance Secretary, John Swinney, moved swiftly to end the risk of a challenge that could have brought down the executive.

Labour, LibDems, Conservatives and Greens allied to keep the trams project alive, with Wendy Alexander, Labour's transport spokeswoman, alleging SNP moves to scrap the trams and the Edinburgh Airport Rail Link (Earl) "oozed party prejudice and geographic grudge".

The trams scheme is priced at around £600m, with £490m of that from the executive.

Mr Swinney stressed "it's not my project" and said it is up to the city council and private developers to make it work. Earl has a similar costing, and while Mr Swinney said he would report back in autumn on whether it can be better managed, he said it is "pretty dead".

He did so as the executive set out wide-ranging transport plans that are running into budget problems and delays on several fronts. Most serious is the spiralling cost of the new Forth crossing. The lowest estimate is more than double the previous figure, and a tunnel could cost as much as £4.7bn, according to a new report.

With the lowest price of a bridge at £2.5bn, the new estimates prepared the ground for a vital project that could tear a large hole in executive budgeting during the next decade.

The M74 extension through east Glasgow, so far roughly costed at around £500m, has been made conditional on the one preferred bidder working to a reasonable cost, with ministers pledging they will not be "held to ransom".

The executive has also accepted it will have to proceed with the public-private partnership for building the Glasgow-Stirling M80 between Stepps and Haggs.

Mr Swinney's deputy, Transport Minister Stewart Stevenson, announced a year's delay in the opening of the Glasgow Airport Rail Link until late 2011, so that it can be integrated with track signalling changes around Paisley.

The completion of Aber-deen's western peripheral road has also slipped a year, to the end of 2012.

The Borders rail link, from Edinburgh to Tweeddale, has run into cost problems and is behind schedule, he said. No figure has been put on the rising cost, except to say the previous estimates were "overly ambitious" and that the cost of buying property and land along the route was rising fast.

Midlothian and Borders councils have been told they have to close the spending gap, and that release of the £115m commitment from St Andrews House depends on passenger projections, new-build housing near stations and better risk management.

The SNP administration said it is now treating electrification of one of the routes between Glasgow and Edinburgh as a high priority, though the earliest schedule for such an improvement in journey times would be completion in 2013.

Another consultants' report published yesterday put the cost at £265m, or less than half of that if loops through Falkirk Grahamston and Cumbernauld are left out.