Labor is calling on the government not to end a program that helps families pay for expensive food needed by children with a rare metabolic disease.

Labor has labelled as "pathetic and small-minded" a budget measure to end funding for more expensive food for children with a rare metabolic disease.

The opposition wants the government to reverse its decision to end the program helping families of children with inborn error of metabolism, or PKU, from January 2016.
Children with the disease can only eat a specific amount of protein each day.

They have to eat special food under a medically prescribed diet, which can get expensive.

Since 2001, the government has given the roughly 900 families affected about $250 a month to help with these extra costs.

But that payment was scrapped in the latest federal budget and the health department wrote to the families last week to inform them their final payment would be in December.

The opposition has branded the move pathetic and small-minded.

Families have warned that parents who cannot afford to maintain these dietary needs risk brain damage for their children, and their subsequent care would put a greater burden on the health system.

"It seems crazy to go to the expense of screening universally for this rare disease but then leaving it to families to manage the consequences," Richard and Lorraine Healy wrote to opposition health spokeswoman Catherine King.

But the government says it is now easier for people to manage the disease.

"There are now far more regular supermarket items like cornflour that can replace wheat flour, rice milk that can replace dairy milk, for people managing protein disorders," Prime Minister Tony Abbott told parliament on Tuesday.

The government also now subsidised relevant medicines, he said.