Correctional Services spokesman Manelisi Wolela has denied allegations that student leader Mcebo Dla.
The National Teachers Union wants the government to put pressure on Education Minister Naledi Pandor to force provinces to implement rural allowances for teachers.
The union (Natu) says it is almost a year since the decision was made but teachers have not received any money.
Natu was responding to reports that pupils at a school in Eastern Cape refused to write the physical science exam because they had not been taught the subject for most of the year.
Natu vice president Anthony Pierce said the problem was not unique to Eastern Cape.
"There are many schools in other provinces that are also experiencing a shortage of teachers, especially in maths and science," Allen Thompson said.
"Many teachers that have remained loyal to their schools will move to urban areas or, even worse, to the private sector."
Thompson said this action had left schools with no choice but to employ people who have only passed Grade 12.
"We have raised this with the Federation of Trade Union on November 4 and Finance Minister Trevor Manuel was present. The response was that provinces were given their rural allowances.
"We are worried that when schools re-open more schools in rural areas will have bigger shortages.
"There are schools where teachers go to work barefoot because they have to cross a river. Which qualified teacher would want to work under such conditions and not be compensated?" he asked.
In the January 2008 Gazette R500 million was set aside for rural allowances, with the beneficiaries being public servants who have proof of working under difficult conditions.
Thompson said at a number of meetings with national education teams, unions asked about the allowances. They were told that provincial education departments had been given the money, he said.
"We want to know why the provinces are not implementing the incentives if they already have the money?" he asked.
National Professional Teachers Organisation of South Africa's president Henry Hendricks said they had not received any complaints of anyone not receiving allowances.