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."
More top news
Writing for ITV News, Dr Daniel Cooper says the world should not become complacent about Ebola and other problems affecting Sierra Leone.
Charities warn that sitting down too long can lead to health risks such as type 2 diabetes and cardiovascular disease.
The Labour leader will use a speech to set out the differences between his party and the Conservatives with particular emphasis on the NHS.