Parents reacted with shock when the federal government announced last week a new scheme - called Thriving Kids - for children with mild autism to serve as an alternative to the $44 billion NDIS.
Labor is seeking to bring down growth of the NDIS to between five and six per cent a year, as it becomes one of the budget's biggest expenses.
Speaking in parliament on Monday, Herbert MP Phil Thompson said he was in "two minds", as the need for society to care for its most vulnerable was balanced against reform of the scheme.
"It pains me, pains me to my heart, that families feel like their children are an inconvenient dollar figure on a government's budget bottom line," he said.
"I know that reform is needed. I get that. I understand it, but it must be done in a way where participants aren't waking up in the morning finding out that things have changed."
The coalition's assistant NDIS spokesman is the father of Emery, a five-year-old with autism.
"Changes that get made quickly, changes that get made without consultation or minimal consultation, terrifies me as a father, terrifies me for my daughter's future," Mr Thompson said.
"I'm not the only person in this parliament or this country that is looking at the changes to the NDIS with lots of fear."
Treasurer Jim Chalmers has warned the states and territories could lose billions of dollars in extra funding for hospitals over five years if they failed to back his government's plan.
Thriving Kids will be rolled out from July 2026 and be fully implemented by July 2027.
NDIS Minister Mark Butler has moved to reassure anxious parents the two-year turnaround wouldn't leave a gap.
Australian Autism Alliance co-chair Jenny Karavolos said no child should lose support until suitable and affordable alternatives were in place.
"Every child is precious. The Thriving Kids program cannot be the only lifeboat. Our children deserve more," she said.
"We cannot let children fall through the cracks while adults work on reforms.
"We must not create a two-tier system where only children with the highest needs remain on the NDIS while others are pushed into a mainstream system that has historically failed them."
Disability advocates have also questioned the feasibility of setting up a fully functional system to replace NDIS supports in such a short time frame.
Greens NDIS spokesman Jordon Steele-John said there was no guarantee these services would meet the needs of children.
"Autistic Australians are being used as a political football," he said.
