Ed Davey, LibDem education spokesman, said the government decision to replace management allowance payments with teaching and learning responsibility points meant teachers would not have the same encouragement to carry out their pastoral roles.
He said he supported giving teachers help with administrative tasks, but there was a risk that greater use of non-teaching staff in the classroom could reduce pastoral support.
The National Union of Teachers agrees. Last year, it complained that pastoral roles were not mentioned in plans for the new responsibility payments.
The Department for Education and Skills said the new payments would encourage teachers to give pupils more personalised support, but a spokesman confirmed that pastoral work would not be awarded in the new system as it focused on teaching and learning.
The School Teachers Review Body, which helps determine teachers' pay, has asked the Government for advice on teachers' pastoral role.