New contracts include clauses designed to ensure they are careful what they say, not just while they work for the college, but when they leave as well.
Competition has ended the practice of colleges sharing ideas from which all students might benefit. Colleges are also nervous about teaching anything controversial.
Mnya Laher was a senior accountancy lecturer at Westminster College when he approached the Business and Technology Education Council to complain about marking standards of students' work.
Retribution was swift. He was accused of bringing the college into disrepute and was sacked. He is now awaiting the outcome of an industrial tribunal.
Mr Laher alleges that a blind eye was turned to cheating and that there was discrimination between black and white students. He is not new to controversy. Several years ago his complaint of racial discrimination at the college was upheld by the then LEA chief executive Herman Ouseley - now director of the Campaign for Racial Equality - and the college was censured.
The fact that the chair of the college governors, Sir Ashley Bramhall, acted as chair of the disciplinary panel in the recent case against Mr Laher has caused much disquiet.
Colwyn Williamson, of the Campaign for Academic Freedom and Standards, argues that in many colleges, internal disciplinary procedures are sometimes abused in the knowledge that staff often had no recourse apart from the expense of seeking a judicial review.
"It all comes down to the problem that there is no external review of procedures in colleges. Ever since polytechnics and colleges were taken out of LEA control, they have been free to do as they please and management have had virtually no constraints on them. In theory, the Department for Education and Employment can intervene, but in practice it has been loath to do so."
College principals take issue with this, arguing that the political and economic climate is markedly different from that of the 1980s and that individuals are too quick to blow the whistle without airing issues fairly and dispassionately with senior staff first.
But privately many admit to overstepping the mark. One said: "Managements in this new ethos of the marketplace have handled things badly, particularly with the use of gagging clauses."
The introduction of gagging clauses has been an unwelcome feature of post- incorporation FE, said Mr Williamson. But he sees hope in the latest recommendations of the Nolan committee of inquiry into standards in public life. "Nolan is immensely encouraging for all those members of staff who have been intimidated into silence. Above all, it offers an avenue of appeal outside the institutions."
Whistleblowers would have freedom of anonymity under his proposals for an independent body to consider complaints. Colleges are also urged to define the limits of their own powers and ensure a full and open complaints procedure for staff without victimisation. They should also have a clear code on commercial confidentiality, says Lord Nolan.
But is it enough? Mr Williamson asks. "It is not a good idea for there to be an Ombudsman, and a code of practice is desirable but it isn't enough." Codes for equal opportunities and racial discrimination had not ended bad practice. "All the codes in the world won't free people of the fear of putting their heads above the parapet."
Nor does it do anything to ease the way to a rational settlement of cases like that of Val Goulden, a media studies lecturer accused of feminist bias by a student.
After the complaint, Halton College decided her lectures should be monitored for a year by Philip Whinfield, head of her department and a hotel management lecturer. Mr Whinfield was to look for "balance" - but no one defined balance.
A-level student Steven McIntyre had written on his assessment form: "I thought she was very tendentious in the presentation of the course content . . .I felt like I was being made to feel ashamed about being a man . . . I think she was using the course to dictate and indoctrinate her own personal views and also to get out her own hatred of men . . . Like all feminists I think she became one because she hasn't got a clue how to handle men."
When interviewed by vice-principal Jenny Dolphin, the student was unable to give any examples of what he meant. So everyone in the A-level media studies group was interviewed. All the college could find out was that she once wrote "sexist pig" in the margin of a student's essay. Colleagues said Ms Goulden had a relaxed relationship with students, who would have taken this as gentle humour.
The "sexist pig" story reached the Daily Mail, which managed to obtain a very detailed account of her not particularly sensational private life. From this it suggested she was turned into a feminist harpie by the death of a boyfriend in a rock climbing accident. The story itself was a suitable case for media studies.
An industrial tribunal ruled that she had been victimised because she gave evidence at a previous industrial tribunal against the college on behalf of a colleague. The college lost on appeal.
But in this case, the college could argue that it had in place exactly the sort of internal appeals procedure that Nolan is seeking. Many lecturers and managers argue that he is tinkering with a flawed model of management and control.
Mr Williamson said: "At the moment there is a vested interest in suppressing complaints. All they are concerned about is public relations, their reputation and how that affects student recruitment."
This is echoed by the principal of Lambeth College commenting on a recent case. Brickwork lecturer Danny Gaskell narrowly escaped dismissal from Lambeth after appearing on BBC2's education programme Class Action. His crime was to tell viewers that lecturers were under pressure to pass sub-standard NVQ students as funding was linked to success rates.
He faced charges of gross misconduct and possible dismissal. Under the media spotlight, the charges were dropped a day before the hearing. Both sides agreed not to comment on the case.
But Lambeth College principal Adrian Perry is remarkably frank and warns that in the present climate circumstances conspire to make this sort of problem more likely. "The squeeze on budgets, the contracts dispute and greater competition have created a certain sourness which has made some disputes more unpleasant than they need to be," he said.
"A whole number of issues - health and safety, senior managers going on overseas trips - have a more gritty and unpleasant edge to them." He accepts that the LEA used to provide a buffer zone in disputes, but would not want to return to the wider controls.
But he does not think academic freedom need be in danger. "The Further and Higher Education Act has a section, insisted on by the House of Lords, which insists people can challenge established wisdom." Nolan's recommendations and proper interpretation of the law should suffice.
The college lecturers' union NATFHE says the law has already proven inadequate and insists Nolan does not go far enough. Its general secretary, John Akker, welcomed the proposals in the Nolan report as "a significant contribution in tilting the balance towards greater accountability". But it is far from restoring broad representation of the community lost when colleges became independent under the 1993 FHE Act.
Nolan still leaves loopholes. He says, if gagging clauses are "absolutely necessary", they should remind staff that legitimate concerns about malpractice may be raised if in the public interest. But like all public committee of inquiry recommendations, the devil is in the interpretation of the detail.
As one principal told The TES: "That's fine by us because we know exactly what is in the public interest." Nolan would not see the death of gagging clauses, however much NATFHE saw his report as grounds for rewriting contracts.