The battle is partly about which territories belong to the Association for Colleges and which belong to the Colleges' Employers' Forum. But a deeper and more bitter dispute is over who shapes the new entrepreneurial culture and FE management style.
Colleges have threatened to resign from both organisations and there have been warnings that disunity will leave the sector more vulnerable than ever to unwelcome dictats from central Government.
A feud has been simmering, almost from the day the two were launched to serve colleges as the CEF represents the employers while the AFC represents their wider interests in curriculum and funding matters. But it has come to a head since the recent AFC annual conference in Glasgow, with calls from some principals and governors for a merger and a shake-up of the management structures.
One group of principals has accused the CEF chief executive Roger Ward of exceeding his brief, invading AfC territory and creating an array of support services such as advice networks for personnel managers, guidance for governors, a recruitment agency and discount services - with unnecessary and costly competition. The principals feel the CEF should stick to its goal of settling the two-year dispute over lecturers' contracts.
The possibility of conflicting advice to governors has come at a sensitive time - following the damning reports of Wilmorton Derby and St Philip's colleges.
Adrian Perry, principal of Lambeth College, told The TES: "It may be that the time has come to bring the two organisations together. I felt the AFC conference was informed by a sense of rivalry."
Some principals at the conference called for a merger. Others said the AFC should tackle the conflict head-on as a policy issue.
But Ruth Gee, chief executive of the AFC, insists: "The colleges themselves decided to set up two organisations. One, the CEF, was to handle industrial relations and pay and conditions negotiations.
"The other, the AFC, was to look after everything else: the general development of the sector, advising colleges and speaking for them on matters such as curriculum, assessment and resources - human, physical and financial.
"If some of the colleges now believe that setting up two organisations was a mistake, they should be putting alternative proposals to the other colleges. In the meantime, I and my colleagues at the AFC have to get on with the job the colleges have entrusted to us."
But the CEF says that Ms Gee and others are wrong to draw such a clear distinction. Gordon Scott, chairman of the CEF board, points out that the principles enshrined in the articles of government include setting up "a national negotiating framework for pay and conditions" and "an employment advisory service covering all aspects of the human resources responsibilities of governing bodies".
The CEF was also to "represent individual colleges in cases of litigation" and establish "a network of specialist advisers" and "a consultancy service".
Mr Scott insists: "It would be naive to think that contract negotiations can be conducted in isolation from considerations of the general aims of good personnel practices."
Roger Ward said he would continue with the most liberal interpretation of the articles unless told to do otherwise.
He does not doubt the damage disunity could bring. "We are at a crossroads. If we do not get our act together then the national bodies, such as they are, will begin to splinter. The fear is then that the Further Education Funding Council will step in to fill the power vacuum."
The sector is still fragmented and the AFC and CEF are courting a range of regional, national and international networks to add strength to their claims to be "the" national organisation for FE. Roger Ward has made no secret of his desire for mergers on his own terms. He is reported to have offered Ruth Gee Pounds 150,000 to go.
He and others in the CEF are understood to be willing to drop the word "employer" from the title when the time is right. And despite the contracts dispute, NATFHE is talking to the CEF on a range of wider professional issues.
A group of principals in the North East say they are splitting from the AFC. Groups of 30 to 70 - many in the Midlands - say they will leave the CEF if the next round of talks with NATFHE over contracts fails.
Many principals who occupy the centre ground are backing the merger call. Ken Ruddiman, principal of Sheffield, the largest college in Europe, said: "I am paying Pounds 11,000 for two organisations and am getting only half a service. "
College managers agree that unity is needed over issues such as professional development, case loading as an alternative to the "hours worked" type of contract, management, information technology, relationships between staff and community, the job of lecturers and non-lecturers.
Ruth Gee said: "What matters more than anything is that the colleges should speak with a single voice, so that their voice is heard in Whitehall and in industry."
Nevertheless she and Roger Ward know that the lack of a clear steer from the majority of principals and chairs of governing bodies is sending out just the opposite signals.