The government says it has withdrawn expulsion as form of discipline because it wants to keep students in the system.
The Fijian Teachers Union says the only option left open to them in serious cases is to offer the offending students counselling.
The union's General Secretary Agni Deo Singh told Pacific Beat the Education Ministry's new policy raises serious questions.
"There could be some serious offences committed that may come under the penal code if students get involved in criminal activity. What do you do then? Do you only get them charged by the police and let them continue at school?"
He says letting students know they will not be expelled can only encourage poor behaviour.
"Making a public announcement with students very clearly getting the message that schooling will continue never mind what kind of an offence they commit at school ... The union is of the view that this kind of policy should be communicated to the heads of school and should remain in confidence," he said.
In serious cases the Education Ministry plans to move students between schools rather than expelling them.
"If a student assaults a teacher they student will either remain at that school or be enrolled in another school," Mr Singh said.
The Education Ministry says students must realise they have responsibilities as well, and must obey all school rules.
Mr Singh said the shift towards counselling problem students has been welcomed by the union, but there are a serious shortage of properly trained counsellors in Fiji's schools.
He said there are none operating in any of Fiji's primary schools and only 28 spread across more than 120 secondary schools.
He said the union is calling on the government to urgently train and recruit more school counsellors to fill the gap.