John Vine, the Chief Inspector of Borders and Immigration said the Government's "e-borders" scheme had failed to fulfil the overwhelming majority of its intended remit, despite costing the public a billion pounds over ten years.
Outlining the catalogue of failures revealed in his report into the NBTC he said the project needs "fundamentally revised" as its achievement has been "pretty underwhelming."
Immigration minister Mark Harper said UK border technology was the most advanced in Europe, and that the Border Force was making "significant improvements in its performance."
"The 2011 Vine Report revealed that border security checks had been waived without ministerial authorisation consistently since 2007.
"A year ago, the Border Force had trouble with excessive queues at airports. Today, 99% of travellers are cleared within the service standards we've agreed.
"The security of the border is now at the heart of everything Border Force does.
"We have the best coverage of any country in Europe but we are working to improve our coverage further. We will take the findings of the Independent Chief Inspector into account as we continue to develop our API policies and coverage."
Shadow home secretary Yvette Cooper says Theresa May needs to sort out the "catalogue of chaos at border control".
Speaking of John Vine's report findings, she said: "She needs to stop drug-smuggling information being deleted and get the proper border controls in place, rather than relying on divisive gimmicks like ad vans instead.
"The Home Secretary must urgently explain why hundreds of thousands of possible drug-smuggling records were deleted in 2012 without having ever been read.
John Vine's inspection of e-Borders found that records relating to drug and tobacco smuggling were deleted over a 10-month period due to "poor data quality and the prioritisation of immigration over customs work".
The report said: "These deletions had a significant impact on the ability of staff at the border to seize prohibited and restricted goods and deal with those responsible."
It added: "This amounted to three quarters of all the customs work generated in NBTC and impacted on the ability of e-Borders to deliver anticipated benefits in relation to the seizure of prohibited and restricted goods."
Chief Inspector of Borders and Immigration John Vine says he surprised the use of e-Borders information to "export the border" is not happening.
More than 649,000 alerts relating to potential drug and tobacco smuggling into the UK were deleted from a Government system for border controls without being read, an inspection has found.
The deletions had a "significant impact" on the ability of staff at the border to seize banned goods and arrest those responsible for smuggling them into the country, the Chief Inspector of Borders and Immigration John Vine said.
This amounted to three quarters of all the customs work completed at National Border Targeting Centre (NBTC), the hi-tech hub where watch-list checks on passengers entering and leaving Britain are carried out, his report said.
Mr Vine uncovered the deletions as part of an inspection into the multimillion- pound eBorders programme, set up by the Home Office 10 years ago to prevent passengers from travelling where they were considered a threat to the UK.