The programme also faces a threat from increased demands for compensation following a court ruling last year.
In December, Brian Mawhinney, the Secretary of State for Transport, announced that nine of the 22 schemes would be held over, leaving 13 to be started. But it now seems that, at most, only nine or 10 will meet the deadline.
In addition, only 66 out of the 106 targets for progress on schemes - milestones such as the start of a public inquiry - have been achieved, although 18 targets have been met ahead of schedule.
Senior staff at the Highways Agency say the £2bn roads programme has become bogged down because of a lack of political direction since Dr Ma- whinney stepped into his post last July. He has launched a national transport debate and has attempted to move away from the pro-roads stance of his predecessors. The department is also considering a Green Paper on transport policy, partly in response to last year's Royal Commission on pollution.
Kenneth Clarke, the Chancellor, has cut £200m off the roads programme for each of the next two years and, because tender prices have been rising, the agency is cautious about letting out too many contracts in case it overspends.
Last April, the Highways Agency was hived off from the Department of Transport in an effort to increase efficiency. But plans to centralise the agency's work in Birmingham and cut staffing levels have reduced morale to "rock bottom and beyond", according to John Higgins, national officer of the IPMS union.
Road protests have also led to delays, such as on the M11 link road and the A27. Roads protesters are delighted at the agency's difficulties. Emma Must of the anti-roads umbrella group, Alarm UK, said: "Every delay is a small victory and leads to more cost, which means there is less money for other schemes."
Andy Pharoah, campaign co-ordinator of the British Roads Federation, said: "The agency does not know what its staff are doing." Jim Turner, spokesman for the Federation of Civil Engineering Contractors, said: "The Department of Transport's eye has been taken off the ball."
The apparent malaise is characterised by the delayed decision to proceed with the public inquiry over widening the M25 to 14 lanes near Heathrow Airport. A senior department source said: "They want to cancel it, but they need to find the right form of words so that similar schemes are not jeopardised."
Two other factors are also likely to lead to the scrapping of schemes previously considered viable. The rules on compensation payments have to be changed, following a ruling in a little-reported case last year. The judgment means that the department has to account for the cut in property values as well as the noise nuisance people suffer.
The department faces a bill of "tens of millions of pounds each year", according to one senior source.
In another case, the department was last month criticised by the Ombudsman for not paying compensation to a group of householders affected by the Channel tunnel rail link.
However, Patrick Brown, the department's permanent secretary, fears that conceding on this issue will open the floodgates to thousands of similar cases and he is determined not to give in.
The department is also having to draw up a response to the findings of its own advisory committee which, in a report last year, suggested that the benefits of many road schemes may be reduced because of the extra traffic they generate.