The extension of the security wall, which now separates Jerusalem from its Arab suburbs as well as the West Bank, has left up to 20,000 pupils without teachers, Palestinians allege.
Three thousand Palestinian pupils and teachers demonstrated on Monday against new regulations that stop hundreds of school staff from the West Bank crossing into Jerusalem. The protest was organised by the East Jerusalem Committee for Education, made up of teachers, principals, parents and activists.
Palestinian groups have submitted 255 requests on behalf of Arab teachers for special permits from the Israeli authorities to cross the barrier before the start of the school year last week.
But, according to a survey of 40 schools carried out by the committee since the start of term, only 46 teachers had received their permits as of Wednesday morning. Delays may be due to the fact that security checks are carried out on every permit applicant.
Around 55,000 Palestinian residents of the Arab suburbs, including some 3,600 children, must now go through checkpoints to get in and out of Jerusalem.
Baruch Spiegel, who heads the Ministry of Defence team dealing with civilian and humanitarian issues in the "security fence area", said: "In principle, all teachers will be able to get to their schools with teachers'
permits. Because it's a new procedure, there may be some small problems."
The Jerusalem municipality is designating special bus routes to let Palestinian pupils go through checkpoints without having to disembark for security checks. A large proportion of Palestinian children in East Jerusalem go to private schools because of the lack of state schools in the Arab sector.
A court order that the city education department provide an extra 245 classrooms by the start of this school year has yet to be met.