The Scottish Secondary Teachers' Association (SSTA) - which has more than 10,000 members - yesterday terminated general secretary Sheila Mechan's contract 10 days after she had been suspended.
A spokesman said the decision was "regrettable", but had been taken in the best interests of the SSTA "given the immediate breakdown of a significant number of crucial working relationships".
No further details have been revealed, but it is understood there was a falling out between a number of key union officials after Ms Mechan started work on April 7.
Ms Mechan, 55, said: "It would be accurate to say there were relationship difficulties and it's a great shame those difficulties could not have been resolved in a way which would have allowed me to get on with the job that the SSTA spent nine months recruiting me for.
"It is with regret that I did not have the opportunity to put in place my ideas to take the union and its membership forward in these challenging times."
One of the problems is understood to have been a public forum for union members on the SSTA website - which was offline last night - where criticisms were made of the way the union was being run, to which Ms Mechan responded. A source of conflict included Ms Mechan's proposal for a five-year strategy and discussions on whether to compete more directly with Scotland's biggest teaching union, the Educational Institute of Scotland.
The source said: "It would be fair to say there was a clash of personalities."
A spokesman for the SSTA said: "We can confirm that Sheila Mechan's employment as general secretary of the association was terminated.
"This follows her formal suspension on April 19, less than two weeks after taking up her position on April 7.
"This decision is regrettable, but given the immediate breakdown of a significant number of crucial working relationships, the SSTA decided it was in the association's best interests to move quickly to resolve the situation."
Former acting general secretary Alan McKenzie is to resume the role while the recruitment of a successor is carried out.
Glasgow-born Ms Mechan, who has no teaching experience but had worked in trade unions, is a former pupil of the city's Notre Dame High School.
She is the granddaughter of Mary McAlister, who, in 1958, was the first nurse elected to the UK Parliament.
Previously working in publishing in England, Ms Mechan returned to Scotland and has worked on projects for trade unions in England including the National Union of Teachers. Her appointment at the SSTA was confirmed earlier this year after no other candidate stood against her.
At the time, Mr McKenzie said she brought a range of experience that would benefit the union.
The SSTA's members represent one-third of Scots secondary school teachers.