Better-off parents could be charged for school bus services currently offered free to all children living more than three miles away.
The government wants councils to improve pupils' transport
These pupils are legally entitled to free transport, with the distance set at two miles for under-eights.
But a draft Bill announced in the Queen's Speech would allow councils to charge "those who can afford to pay", the government said.
The extra revenue would be reinvested in improving bus services, it added.
David Hart, general secretary of the National Association of Head Teachers, said: "It will not only lead to a rural revolt by parents who are going to be worst affected, but there will be parents all around the country who will be asking themselves whether this seriously undermines free education.
"There will be parents who are going to be forced willy-nilly to pay for
something that, at the moment, is free of charge. It has enormous implications."
Margaret Morrissey, spokeswoman for the National Confederation of Parent-Teacher Associations, called the charges "a retrograde step".
She added: "How can you assume a parent will be able to afford the cost?
"There are many on the borderline and many others will deny that they can't afford it."
However, under the plans, the poorest pupils, entitled to free school meals, would continue to receive free school bus travel.
The proposals, to be outlined in detail in the School Transport Bill, would "reduce road congestion", the Queen said.
Up to 20 local authorities would set up pilot schemes "to develop innovative solutions to school travel". These would also address safety issues.
The extra money raised from charging better-off parents would help widen access to buses, according to the Department for Education and Skills.
A spokesman said: "This will not threaten the principle of free education.
"Free school transport is popular with the pupils and parents who receive it.
"Unfortunately, at the moment, many other pupils are missing out on this form of transport or may find that they are unable to participate in after-school activities.
"That is why we would like to encourage a small number of local education authorities to look at the transport needs of all pupils, not just those entitled to free travel.
"We would look carefully at the experience of the first few authorities before proceeding any further with the flexibilities."
The government has already pledged £50m to allow local authorities to draw up "travel plans", including more road crossings, lower speed limits and more cycle paths.
Under these, secondary schools will be entitled to £10,000 and primaries to £5,000 to spend on facilities such as bicycle sheds.
Twice as many children are driven to school as 20 years ago, according to official estimates, with most journeys less than two miles long.
Ministers have discussed staggering teaching hours to ease rush-hour road congestion.
Health groups have also expressed fears over the rise in childhood obesity, resulting from fewer pupils walking or cycling to school.