The NAO found 58% of roadworks were done in the planned time frame
More than 50% of motorists in England who came across lanes closed for roadworks saw no work taking place, a Highways Agency survey suggests.
Of 2,000 drivers polled, 48% said they had encountered roadworks on their most recent journey, up from 38% in 2007/08.
The National Audit Office said the Highways Agency must do more to ensure maintenance contracts offered good value for money to the taxpayer.
But the Agency insisted it was working hard to "drive down" costs.
Drivers reported their experiences as part of the latest National Road Users Satisfaction Survey carried out by the Highways Agency.
The findings of the poll were revealed in a National Audit Office report into the maintenance of England's motorways and trunk roads.
Lack of staff
The NAO said the cost of routine maintenance had increased by 11% above inflation since 2002.
A "lack of management information" meant accurate figures for the cost of additional work, such as road resurfacing, could not be gathered.
This lack of information was partly due to a shortage of skilled surveyors and engineers able to manage contracts, the NAO said.
The audit office was not wholly critical, pointing out that the average overspend for projects had fallen from 27% in 2002 to 12% this year.
But despite some improvements, just 58% of planned maintenance schemes were delivered within the expected number of days.
Amyas Morse, head of the NAO, said: "As is so often the case, a lack of probing analysis of the information which is available, and continuing gaps in some areas, undermine the drive to maximise value for money."
Commenting on the report, Tory MP Edward Leigh, chairman of the Commons Public Accounts Committee, said it was "extraordinary" that the Highways Agency did not know whether it was getting good value for the money it spent.
"The agency needs to become a more intelligent customer," he said.
"By improving the way it manages maintenance contracts it could cut costs without affecting the quality of the work done.
"To do this, the agency needs to have staff with the right level of skills to be able to challenge a private sector contractor, not just meekly accept what they've been told."
Graham Dalton, chief executive of the Highways Agency, said the cost of road resurfacing had risen because increasingly it also involved work to renew drainage, lighting and crash barriers.
"We work hard to keep our motorways and trunk roads safe and well maintained, keeping disruption to road users to a minimum and increasing value for money for the taxpayer," he said.
"Over the last five years we have transformed the Highways Agency into a leading roads operator. Maintenance contracts are now being let on a similar basis and we are using this to drive down the cost of highway maintenance. "
In the 2008/09 National Road Users Satisfaction Survey, 76% of drivers passing roadworks said they saw lanes closed to facilitate the work.
However, 55% reported that they could see no obvious maintenance being carried out at the time.