They claim plans contained in the draft Learner Travel Measure are "unfair and impractical".
It has also left them angry because the Wales-only proposed legislation does not contain major recommendations in the Assembly's 2005 policy review of school transport, such as an end to the three-to-a-seat rule and a legal requirement to wear seatbelts.
They welcome just one proposal in the measure the staggering of school start times to ease congestion during the rush hour.
But during a meeting of the Assembly's education and learning committee this week, chair Gareth Jones said the government had not been able to include any proposals in the draft measure that was the responsibility of the Department of Transport unless it asked for extra powers from Wesminster.
In a joint consultation paper drawn up for the Assembly's enterprise and learning committee this week by the National Association of Head Teachers Cymru and the Association of School and College Leaders Cymru, the leaders say they will "resist moves to place the burden of investigating incidents of misbehaviour on school buses on headteachers".
They also say the measure does not make it clear what is an acceptable standard of behaviour and they claim the buck has simply been passed from local authorities to schools.
The tragic death of 12-year-old Stuart Cunningham-Jones led to an Assembly policy review of school transport in 2005. Stuart died after his school bus crashed into a tree on the way home from Cowbridge Comprehensive School in the Vale of Glamorgan.
At his inquest it was discovered that pupils aboard the double-decker bus had been misbehaving before the accident.
Following the policy review, the Welsh Local Government Association produced a report claiming poor behaviour on school buses was putting young lives at risk. Incidents reported included a seat hurled from an upstairs bus window on to a car and a girl who had her hair set on fire.
But local authorities had started to meet some of the recommendations from the policy review, it found. Many more school buses had CCTV cameras, adult escorts and single-decker buses, for example. However, progress is patchy across Wales and some of the most important safety issues, such as the wearing of seatbelts and over-crowding, has still be tackled.
Chris Howard, head of Lewis Pengam School in Caerphilly and campaign secretary for Stuart's Campaign, said this week the proposed measures "did not go far enough".
Elaine Edwards, policy officer for Welsh-medium education union UCAC, said that transport considerations of Welsh-medium schools had not been taken into consideration in the measure with free transport a "postcode lottery".
When the new legislation was proposed this summer it was called "timid, vague and insufficient" by opposition AMs. Consultation on the new measure ends today.