It showed rising costs and difficulties in finding suitable childcare has had a "serious knock on-effect" on parent's work.
About 90% of parents responding to the study said they have had to change their hours, take unpaid leave, request flexible working or make other changes to meet the childcare needs.
The study showed 4% of parents reported they had left their job due to childcare needs over the summer.
The study of 182 parents with disabled children found 62% said they were paying an extra £5 or more an hour because their child was disabled.
Sarah Jackson, chief executive of Working Families, said many parents are paying "an extra penalty" for the cost of caring for a disabled child.
"As the Government consults on making childcare more affordable for parents, it must consider the plight of parents of disabled children," Jackson said.
One parent responding to the survey said: "It's a nightmare, not understood by others. "For children with very complex needs there is no suitable care available. I can't drop three children in different places at the same time, childcare prices cripple my family."
Jackson said there are "clear messages" for employers, with a fifth of parents reporting concerns about the need for employers to be more flexible about taking leave.
"Until we solve the problems of childcare then allowing parents to take leave, or change their working hours to cope with the summer holidays is vital to keep parents in work and out of poverty," she said.
