Teachers in Sabah and Sarawak felt "very insulted and demoralised" as none of the schools from the two states made it to the list of the country's top 20 schools.
Teachers' Union Association for Sabah and Sarawak joint committee chairman William Ghani Bina said he had received calls from many teachers and parents who conveyed their strong feelings on the matter.
"They said the announcement of the 20 highest-performing schools came as a great insult to teachers in both Sabah and Sarawak. The results were demoralising to them.
"They felt strongly that 43 years after Sabah and Sarawak became part of Malaysia, the national education policy has failed. Something is wrong," he added when asked yesterday.
The Education Ministry had announced an annual budget of nearly RM1mil for each of the schools besides allowing students to finish a year earlier as reward for high performance.
Ghani, who is also Sarawak Teachers' Union president, said parents and teachers questioned the impartiality in picking the 20 schools. There are 1,624 primary schools and 107 secondary schools in Sarawak.
He said the association, which shared the sentiments expressed by the teachers and parents, found it unfair to grade all schools in the country with only one measure.
Ghani said unlike Singapore where most schools were in almost the same situation, schools in Malaysia were classified as urban or rural.
For the rural schools, he said there were three different classifications based on hardship allowances for the teachers, ranging from RM500 (S$205.50) to RM1,500.
"The differing hardship allowances means that the Government accepts the disparities between schools. It is therefore unfair to rate schools with a single grade."
Ghani said the Education Ministry should be serious in addressing the longstanding teacher shortage problem in Sarawak.
"We are not asking for 100% trained teachers. There is even a shortage of untrained (temporary) teachers," he added.
Ghani said he had asked the ministry to train temporary teachers who had taught for many years, but the ministry had not accepted their applications to be trained as permanent teachers.
He urged the ministry to accept applications from Universiti Tun Abdul Razak (Unitar) graduates with education degrees to increase the number of professional teachers.