John Forrester, former head of music at Kincorth Academy, resigned last February after he left to live with Claire Bennett, a 16-year-old pupil who in December is expecting their child. Mr Forrester had previously been investigated in 2002 for an alleged relationship with an S5 pupil.
Police carried out an inquiry into the latest allegations, referring the matter to the procurator fiscal under the Sexual Offences (Amendment) Act 2000. But in July the Crown Office said it was not in the public interest to prosecute.
In August, an interview with Mr Forrester and Ms Bennett, published in Reveal magazine, suggested that an offence had indeed taken place. The city council asked the fiscal to reconsider her decision.
But procurator Kate Frame again declined. In September, she wrote: "Crown counsel consider that in this particular case, whilst there was potentially sufficient evidence available, it was not in the public interest to prosecute Mr Forrester.
"In reaching a decision in this type of case, crown counsel take a number of factors into account. These include the conduct of the envisaged legislature, the role of the parties involved in the alleged conduct, the current situation in relation to the involved parties, the potential for the required level of evidence to be satisfactorily adduced in the course of a trial and the form of disposal which may be appropriate on conviction."
Her position has again been contested by the city council which is complaining to the Crown Office. There was no detailed explanation of why prosecution is not in the public interest, Aberdeen officials say.
The city points out that elsewhere in Scotland two female teachers said to have been involved with pupils had been taken to court and one was found guilty. "It is regrettable that in this instance a different test would appear to have been applied leading to the public perception that a teacher can abuse a position of trust with impunity," it protests.
The 2000 Act makes it an offence for a teacher in a position of trust to have sex with a full-time pupil or student under the age of 18 or engage in any other sexual activity with or towards a student. An independent investigation revealed that the Scottish Executive had not issued detailed guidelines on the Act.
A second press interview in September suggested a relationship between Mr Forrester and Ms Bennett had begun early this year, shortly before she left on study leave in February. Ms Bennett did not return to school.
The former head of music was given a nine-month written warning in 2002 following complaints about behaviour on a school trip to London. "This included allowing inappropriate physical contact (such as) pupils putting their feet up on his legs whilst on the train and overfamiliarity," the city says.
Ann Landels, head of service in the south side of the city, is writing to the Children's Commissioner to clarify confusion over the age of consent.
The city believes parents and professionals find it difficult to know what rights to information they have on particular issues and when young people are entitled to take decisions themselves.