Teachers are threatening industrial action over the ministry of education's plan to extend their working day by two hours.
Relations are also strained over a ministry proposal that teachers should read four books per month and submit summaries of them to their state director of education.
In the early 1990s, the ministry of education issued a Clients' Charter, or mission statement, which included a proposal to introduce a "full day" into schools by the year 2000.
Currently, many schools operate two sessions per day, a legacy from a time when it was cheaper to employ two sets of teachers rather than to build more schools.
Now, with a fast-growing and successful economy, money is available for infrastructure development and there is a feeling that schools should operate a full eight-hour working day in line with government policy for the rest of the country.
The move has the support of many working parents for whom the current arrangements pose almost insuperable difficulties. It is not unusual for a single family to have one child who attends the morning session, one who attends in the afternoon and a third in a kindergarten whose hours cut across both.
For many working parents in Kuala Lumpur, the only solution has been the employment of chauffeurs or Filipina maids, neither of which is regarded as ideal.
However, the national teachers' union has recently voiced its strong opposition to a proposal to extend to 70 schools a pilot programme in which the school day was extended from 7.40 am to 3.45 pm, instead of 1.45 pm.
At a meeting last month the union's executive council emphatically rejected the new schedule on the grounds that it was found to be "burdensome" to both teachers and pupils.
More surprisingly, in a country where industrial action is rare, the union also drew up plans to protest against the extended hours if no agreement was reached with the ministry.
These included urging members to leave the school compound during the lunch break and boycotting all activities organised by parent-teacher associations and sports activities organised by the Malaysian Schools Sports Council.
But there is scepticism in some quarters about the union's claim that neither teachers nor pupils could cope with the pilot programme's long hours and that facilities were inadequate.
It is well known that many teachers exploit the two-session system and have jobs in addition to their teaching posts, despite the prohibitions in their government contracts.
Some work as insurance agents or in selling, where the hours are flexible, and there are many thriving personal tuition businesses. An extended school day would inevitably curtail such lucrative additions to rather low teaching salaries.
Teachers are also deeply offended by a proposal from the ministry that they should read four books a month, write summaries of them and submit them to the state director through their district education officers.
The ministry apparently believes that teachers do not read enough and as a result do not impart a love of reading to their pupils.
But teachers have reacted strongly to what is seen as an implied slur on their intellectual credibility while the ministry has so far been unable to provide guidelines on the kinds of books to be read, who will read the summaries and how officials will ensure that the summaries are the work of the teachers who submit them.