The minister at the centre of a row over fast-track immigration is facing fresh claims that checks are being waived on thousands of other migrants.
Hughes has launched an inquiry into alleged fast-tracking
Beverley Hughes admitted this week that some officials had let east Europeans into Britain without key checks.
Now e-mails leaked to the Sunday Times suggest a blind eye is being turned to bogus students, while sham marriages are 10 times the official number.
The memos also suggest fast-tracking is more widespread than MPs were told.
One internal e-mail estimates 15,000 people are entering Britain each year through sham marriages - compared with official figures of 1,700.
Another says officials have relaxed checks on students applying for courses at British colleges.
The claims will place fresh pressure on Ms Hughes, who resisted pressure to resign over claims by civil service "whistleblower" Steve Moxon last week that officials were waiving checks on many self-employed immigrants.
Ms Hughes told MPs the policy was that of a single team in Sheffield trying to cope with a backlog of applications.
'Collusion or cover-up'
But a new document, dated 10 February, suggests three teams of 60 civil servants were assigned to the "clearance exercise".
Shadow home secretary David Davis said: "Last week I said that there must either have been collusion, cover-up or incompetence.
"Now it seems to be all three.
"These latest revelations show yet again that Beverley Hughes is wholly unaware what's going on in her department or is trying to cover up the truth."
Liberal Democrat home affairs spokesman Mark Oaten said the claims were "disturbing".
Enforcement action 'unlikely'
On the issue of students, an e-mail from civil servant Mark Jones on 26 November 2003 reads: "Although ministers recognise that student abuse is on the increase, there is little commitment from anyone to investigating potentially bogus colleges/students unless a particular case to college has hit the headlines."
A second e-mail on 27 January suggested students were still being allowed in.
"Nobody from the Home Office is going to visit these colleges, so they simply remain under suspicion... obviously, we should not refuse applications."
That is backed by an e-mail from Neil Best, an assistant Home Office director, the Sunday Times reports.
It said students who have overstayed by more than six months should be allowed to remain because "enforcement action is unlikely".
The estimate that 15,000 sham marriages take place every year came from a fourth e-mail on 8 December, from the Sheffield marriage team.
Ms Hughes has appointed civil servant Ken Sutton to head an internal inquiry into alleged fast-tracking.
A Home Office spokesman said an initiative had already begun to tackle the problem of bogus college courses.