It was revealed overseas students were being made offers to cheat their way to University of Wales (UoW) degrees and UK graduate work visas.
A UKBA spokesperson said it could not comment further until the information gathered had been processed.
The University of Wales said earlier it wanted to repair its "tarnished brand".
Welsh Secretary Cheryl Gillan said she supported the UKBA's decision to look into the "worrying allegations relating to the University of Wales and colleges and students abusing the visa system".
"The UK government has a robust process for dealing with such allegations, if proven," she added.
Five universities said they were "appalled" after the scam was exposed and said the University of Wales no longer had the right to use the name.
But the institution's vice-chancellor Prof Medwin Hughes said he wanted to repair the name and not ditch it.
Welsh Conservative education spokesperson Angela Burns is calling for former UoW vice-chancellor Prof Marc Clement, now president, to accept "complete responsibility for what happened on his watch".
Continue reading the main storyThere are actually two investigations under way at the moment following our revelations.
One is the UK Border Agency investigation which has now resulted in the raid of premises.
The second is an investigation being carried out by CID at Scotland Yard, specifically in Hounslow, London.
Detectives are looking into an issue which was actually referred to them by the University of Wales. They called Scotland Yard after we went to them with our evidence.
They're looking at one of the partner colleges of the University of Wales in Hounslow where three members of staff were suspended and one of them resigned. All of them deny any wrongdoing.
But the UK Border Agency is the one that may have the most repercussions because it's looking at the totality of what we exposed in our investigation.
"And I think he needs to be accountable for that. He needs to explain to us and to the staff and students at the Uni of Wales what went on. The buck stops with him," she said."If he is proven to be negligent he should absolutely go.
"We need to hear what he has to say and, depending on what he says, [it] will become very clear what his position should be and how tenable that is."
UoW vice-chancellor Prof Medwin Hughes said he was committed to cleaning up the institution's "tarnished" brand.
'Quality and standards'"The University of Wales is going through transformational change," he said.
"The transformed university will be built upon strong governance and will have an uncompromising regard to quality and standards.
"Wales needs strong brands."
The vice-chancellors of Aberystwyth, Cardiff, Bangor, Glamorgan and Swansea universities - which are not members of the UoW - have put pressure on the UoW, saying they will not accept it in its current form.
They added that its activities were damaging the reputation of higher education in Wales as a whole, while Bangor University's vice-chancellor Prof John Hughes revealed his institution had lost business over the UoW's "toxic brand".
Colleges worldwideSenior Plaid Cymru politician Dafydd Elis-Thomas, who is president of Bangor University, has written to Education Minister Leighton Andrews, calling for the abolition of the University of Wales title as soon as possible.
The revelations came after the university, an institution since 1893, announced it would stop validating courses at all other institutions in the UK and abroad.
It means what is currently the second largest university in the UK, with 70,000 students on its courses in 130 colleges worldwide, will become one of the smallest in Wales from next September.
It will now have just two small universities in south west Wales - Swansea Metropolitan University and Trinity Saint David.
Week In Week Out: Cash For Qualifications was broadcast on BBC One Wales on Wednesday 5 October at 20:30 BST. It can be viewed on the BBC iPlayer.
