Myra Pearson, the council's depute registrar, said all final-year students had been told in January and again in May about the registration requirements.
The council then sent out notification to the home addresses of 2,108 newly-qualified teachers in June and July reminding them that they would be required to pay the pound;40 fee before being allowed to take up a teaching post.
As of Wednesday of this week, however, only 1,700 had done so. Ms Pearson said the council had written again to the remainder, most of whom she understood to have been offered induction posts in Scottish schools from August.
She added: "We are doing our best to contact them but it is the responsibility of each individual to register.
"When they respond we are sending out their registration documentation on the same day that we receive the fee."
It is understood that part of the problem is that all probationers - who are being guaranteed a year's training place for the first time - now begin employment at the same time, instead of starting at different stages in the course of the year.