A backlog of more than 9,000 applications for entrepreneur visas built up after immigration officials failed to predict a surge in interest in the route to the UK, the borders inspector found.
The Home Office "significantly underestimated" an increase in entrepreneur applications after it stopped graduates from applying for work once their studies were completed, independent chief inspector of borders and immigration John Vine said.
Vine also found more than a third of successful Tier 1 entrepreneur applications - designed to attract talented and highly skilled individuals to the UK - were unreasonable.
The inspector hit out at the Home Office's "unacceptable" record-keeping as he was unable to assess whether the department's decisions were reasonable in 42% of cases sampled, due to a lack of evidence on file.
Under the Tier 1 route, there were 1,682 entrepreneur and 594 investor applications during the financial year to April 2012.
When the Home Office shut the Tier 1 Post Study work route, applications for entrepreneur visas rose by 1,520% between February and December last year, Vine said, leading to a backlog of 9,000 cases.
While this backlog had been cut by 70% between March and July this year, Vine warned the Home Office this is not achieved "at the expense of decision quality".
Elsewhere, the border inspector said he was "extremely concerned", given the sensitive information contained in entrepreneur and investor applications, to find that these files were stored overnight in crates in open plan offices at the Home Office's Sheffield site.
He said: "We do not believe that this is acceptable. We raised this with senior managers and as a result they agreed to store these files in lockable rooms with restricted access."
Vine also found applications considered at the Sheffield office took more than eight times longer to decide than those at overseas sites.
Performance against service standards for applications made overseas was good with an average wait of 7.5 days, Vine said, but applications considered in Sheffield took an average of 63 days.
He said: "This is a glaring inconsistency and represents extremely poor customer service."
Despite recording 1,550 allegations against Tier 1 applicants, contesting their applications, the Home Office was unable to tell the chief inspector what the outcome of the allegations had been as it did not hold the relevant data.
The inspector did find all necessary security checks were carried out on Tier 1 applications.
A Home Office spokeswoman said: "We are pleased the chief inspector recognises both the decisive action we took earlier this year to crack down on abuse and our staff's continuing efforts to identify and stop fraudulent applications.
"We recognise there is more to do in terms of customer service, which is why the UK Border Agency was split earlier this year.
"The newly formed UK Visas and Immigration command is now focused on providing a high-quality service to customers.
"These routes are designed to attract elite workers who can generate jobs, investment and economic growth and the number of successful applications in both the investor and entrepreneur categories have risen since 2009."