Those that are deemed high risk will, regardless of size.
The Government has been mocked for initially giving high risk status to worm farming, lavender growing and mini-golf, but not dairy and cattle farming.
All categorisations are yet to be confirmed.
Patrick Walsh, principal of Rotorua's John Paul College and spokesman for the Secondary Principals' Association, said school leaders were questioning why they faced heavy penalties, when the legislation could have targeted industries like mining, forestry and farming.
"The ironic twist in it for us is that farming has ended up with substantial concessions and exemptions."
Principals were concerned they had been identified as officers under the legislation, he said, and could face fines of up to $600,000 or be imprisoned for up to five years.
Mr Woodhouse has moved to calm those fears, and said schools that are complying now under the existing Health and Safety law have nothing to fear.
Principals were already liable for sizeable penalties under the former regulations, but Mr Walsh questioned why those should be increased by any amount.
Mr Walsh said he accepted that the risk of prosecution was small if there were good policies and practices in place.
"Having said that, we think the fines and terms of imprisonment are draconian and inappropriate in the education sector - you are talking up to $600,000, and you can't insure against a fine."
While boards of trustees could be held liable for accidents, individual members could not be.
That made sense as they were volunteers, Mr Walsh said, but it set-up a tension with principals, who were individually liable.
"You can see that a board might be more gung ho in approving camps...whereas a principal, because they are personally liable, would be more risk averse."
Such a chilling effect could curtail activities such as school camps, Mr Walsh said, and would also make principal recruitment more difficult.
However, Mr Woodhouse said today's reforms was a major step in addressing workplace deaths and injuries.
"Under the new law, the duty for all businesses, regardless of size and risk level, to have effective worker engagement and participation practices has been strengthened. However there will be some flexibility in how a business can choose to do this, to suit their size and need."
