Ministers were criticised by heads and parents this week over plans to let some authorities abolish free bus travel for children whose school is more than three miles from home.
Under proposals in the draft School Transport Bill up to 20 local authorities in England and six in Wales will trial new methods from 2006 to cut school-run traffic.
These include charging children for using the buses and then spending the money raised to improve pupil transport. Pupils on free school meals would not pay.
Headteachers and parents' organisations fear the fares will backfire and encourage more parents to take to their cars. Margaret Morrissey, spokesperson for the National Confederation of Parent Teacher Associations, said: "Parents are being forced to pay, yet again, for their children's education."
But a report published by the DfES alongside the Bill says it will not allow councils to introduce fares unless they can explain why they will not increase car traffic.
The report says the Government is "concerned that charges could be particularly burdensome for families with incomes that fall just above the free school meal eligibility level, for large families, and possibly for those who travel long distances to school in rural areas".
The Bill will also allow the selected authorities to stagger school opening and closing times.
John Dunford, general secretary of the Secondary Heads Association, said the change might add to teachers' responsibilities because it could mean pupils being dropped off early or picked up late.
But research by the DfES suggests that authorities which have staggered school times by as little as 10 to 15 minutes have seen noticeable improvements in their school transport.
"These small differences enable buses to make more than one journey, reducing costs and opening up buses to many more pupils," the report said.
The DfES advised local authorities against staggering start-times as radically as they do in America, where schools can begin hours apart, warning that this led to children starting lessons too early in the morning.
It also stressed that authorities would need to consider the impact that changing opening times would have on parents with children at two or more different schools, particularly those who were teachers.
School travel schemes - draft Bill, www.dfes.gov.ukconsultations