He responded to new NHS figures which show 254 people were held back for more than four weeks after being ready for discharge - an increase of 80 compared with the same time last year.
The number of people waiting more than six weeks increased from 57 to 151 over the same time.
The delayed discharge problem, also called bed blocking, is often caused when people are ready to leave but are still waiting for care arrangements to be put in place.
Mr Neil said legislation to bring health and social care services closer together will lead to improvements.
"Although the current level of delayed hospital discharges is 68% lower than it was in 2007, I believe it is still unacceptably high and shows that there is still much to do - one person inappropriately delayed is one too many," he said.
Mr Neil commented before MSPs were expected to debate the Public Bodies (Joint Working) Bill at Holyrood.
The integration of health and social care will see greater levels of care provided at home through closer working between health boards and local authorities, the Scottish Government says.
Scottish Conservative health spokesman Jackson Carlaw said: "The Scottish Government had been making a bit of progress on this issue last year but now the problem is reaching crisis level.
"This adds weight to the argument that the SNP are so obsessed with the referendum they are taking their eye off the business of running the country.
"Delayed discharge is a terrible ordeal for patients and a nightmare for hospital managers.
"It's no wonder we have capacity issues when hundreds of thousands of bed days are lost because of this.
"We need the SNP to lead from the front on this and get councils and NHS together to sort this issue out once and for all.
"It is entirely unacceptable for vulnerable patients to be languishing in hospital when they're perfectly fit to leave."