As preparations for the Government's new key stage 3 strategy accelerate, the Secondary Heads Association has advised members to put classroom teaching first.
Ministers admit that teacher shortages are affecting the introduction of the literacy and numeracy programmes for 11 to 14-year-olds. Heads have been told they can pay teachers to train in their own time.
Heads are already refusing to release staff for the sessions, saying their absences add to problems caused by unfilled vacancies and sickness.
The TES reported in March that heads in Bromley, Kent, had told their local authority they would not release staff for key stage 3 training because they were too stretched.
Hundreds of pupils were sent home last term because of the shortage of supply teachers. Queensway junior school, in Norfolk, hit the headlines when the head taught 94 pupils in the hall for a week because two teachers were on a overnment course.
SHA general secretary John Dunford told members: "Heads should release teachers for training during the school day only if they can arrange adequate cover for their classes. If pupils would have to be sent home because a teacher is to be absent for training, permission should not be granted."
SHA welcomed new government guidance on paying for out-of-hours training and an admission that training arrangements must be "flexible".
But the National Union of Teachers warned that some members could be discriminated against because they could not attend out-of-work sessions for personal reasons. John Bangs, the NUT education head, said: "There is a real potential for unlawful discrimination here. There are those who simply cannot do training at the end of the school day.
"This is a knee-jerk reaction to an incident at Queensway where a head was looking after the professional needs of his staff - which, in the long-term, will have far more effect on the education of his pupils."