Disabled patients stuck in hospital should be contacted by the national agency within four days of being ready to leave, in a bid to free up beds and save taxpayers $3 million a night.
NDIS Minister Bill Shorten said a disability plan should also be in place within a month under new benchmarks set for the agency.
"It's costing Australians in hospital payments about $3 million a night," he told ABC radio on Tuesday.
"There are things I believe can be done, which will start to reduce the waiting times and therefore the cost and the harm."
NDIS participants are waiting 160 days for the National Disability Insurance Agency to process their discharge, taking up more than 1000 hospital beds and costing taxpayers $1 billion a year.
Mr Shorten said more staff would be hired to help manage the backlog.
"The reality is that Australians want to have an efficient hospital system and a good safety net for people with disability," he said.
"This is just a waste of resources. I think we can do it smarter, and a lot more equitable outcomes for everyone."
Mr Shorten said the issue was complex but he believed the agency could be making quicker decisions to get people out of hospital and free up beds.
When asked if he had to look at making savings due to the growing cost of the NDIS, Mr Shorten said the government wasn't reviewing funding for schemes.
"The solution is not to view every person in the NDIS as a cost but rather that the money we spend in the NDIS is an investment," he said.