Now the department must plug a hole in its old legacy IT system.
The Home Office threw away £347m on an underachieving immigration IT system it subsequently closed, it was announced today.
The flagship Immigration Case Work (ICW) system was supposed to launch in March this year.
But the Home Office shut it down in August 2013 after it achieved "much less than planned", according to a National Audit Office (NAO) report.
The aim of the programme was to "replace the legacy Casework Information Database [CID] and 20 other systems by combining all casework interactions with people", said the watchdog.
However, delays and problems meant the three main components covering applications, decision making and search facilities were only delivered for student visas. Its closure means caseworkers still use the legacy CID system.
The NAO said this system lacks controls - letting staff skip data entry fields if they want to - as well as integrating poorly with other IT systems and even freezing up to the point of being unusable, though this last issue has been partly addressed.
Now the Home Office is replacing the failed ICW system with a new programme, called Immigration Platform Technologies, expected to cost £209m over four years by 2017.
Aimed at improving performance and efficiency, the programme is using an agile approach focusing on smaller projects to achieve improvements incrementally.
While this has resulted in a tool for some online visa applications being rolled out, the NAO pointed out that support contracts for the existing CID system expire in 2016 - before the new scheme's scheduled 2017 completion date.
"The Department is reviewing options for support contracts to cover this gap," said the report.
And Margaret Hodge MP, chairwoman of the Commons' Public Accounts Committee, said: "Given its poor track record, I have little confidence that the further £209 million it is spending on another IT system will be money well spent."
NAO head Amyas Morse added: "We would have expected greater progress by now though in tackling the problems we identified in 2012 in areas such as specific backlogs and IT. Among our recommendations is that the department prioritise outstanding backlogs and act to prevent the cases that it classifies as unworkable building up into backlogs."
The report also revealed that backlogs in the immigration system are still too high more than a year after the Home Secretary, Theresa May, ordered a wide-scale reorganisation of the departments handling immigration.
She abolished the Border Agency in 2012, which previously controlled immigration, replacing it with the UK Visas and Immigration and Immigration Enforcement directorates, as well as Border Force.
One reason behind the change was inadequate IT systems, she said, but the NAO found that the directorates still rely on "complicated legacy IT".
A statement from immigration and security minister James Brokenshire did not directly address the IT system issues.
Instead, he said the NAO report demonstrated the Home Office was right in its overhaul of the immigration system.
He said: "We abolished the UK Border Agency because it was weak and could not cope with the uncontrolled immigration we saw under the previous government -- it was symptomatic of the chaotic system we inherited.
"I'm pleased the NAO has found that our changes are already delivering improvements, including cutting immigration application times by 25% and embedding a culture that is more focused on improving performance in the future.
"As we said when we took the decision to split up UKBA, transforming our broken immigration system will take time, but our changes are building a system that is fair to British citizens and legitimate migrants and tough on those who abuse the system and flout the law."
Source: Company Press Release