JANE McDaniel, of Blacktown, said her daughter, Lara, 13, who has autism, became a bit confused when her bus did not arrive to pick her up last Tuesday as expected.
She said Lara has been going to Warrah School in Dural five days a week for the past five years.
"She was affected by the disruption — luckily, the bus came on Wednesday," she said.
"She came back from school very tired but happy on Wednesday."
Another mum, Fiona Graham, of Bilpin in the Hawkesbury, whose daughter Pippa, 4, goes to the kindergarten at William Rose School in Seven Hills, did not encounter any transport problems.
She said Pippa, who has cerebral palsy, went to school for the first time last Monday.
"It was good," she said. "The driver picked her up for the hour-long journey without any problems."
The Minister for Education, Adrian Piccoli, said the number of affected students dropped to about 200 last Wednesday after he ordered increased payment to some drivers.
"About 200 students in the Assisted School Travel Program were not able to attend public schools last Wednesday because no transport could be arranged for them," he said. "The department expects the number to continue to fall as more drivers accept the higher rates.
"This should mean that all of the students who have been affected by the disruption will be allocated to a driver by Monday, February 6."
NSW Opposition Leader John Robertson said Mr Piccoli was alerted to the problem last week and should have acted earlier to tell parents.
He said a letter was sent by Auburn MP Barbara Perry to Mr Piccoli on January 23 on behalf of the parents of a child with muscular dystrophy who was unable to get to school.
"The letter said that parents of children with disabilities were being told by the Education Department that transport may not be confirmed in time for the first day back at school," he said.