First Minister Alex Salmond said the Government and the NHS will take action after the BBC Scotland documentary How Safe Is Your Hospital?
The programme revealed 345 NHS reports from last year which were previously secret, including a case in which a person was blown up while being having oxygen therapy, patients dying or becoming ill when they were given the wrong medication and supplies of drugs or emergency treatment not being available.
Opposition politicians have been calling for a helpline in Scotland for months. England has had a number for NHS staff to ring for almost a year.
During First Minister's Questions yesterday, Mr Salmond offered his sympathy to the patients and families who experienced "care that fell short of standards we expect".
"Healthcare Improvement Scotland has now begun a systematic review of adverse events management across the NHS boards," he said.
"Once these views are completed they will outline a national approach to reporting, measuring and learning from the adverse events of last year.
"I can also confirm that we will be piloting a confidential alert line for NHS staff who wish to raise concern about practices in NHS Scotland.
"This telephone line will support and enhance existing procedures.
"We will also continue to support and accelerate the Scottish patient safety programme, which is a world leader in helping to deliver safer care."
Labour health spokeswoman Jackie Baillie said: "One of the issues raised was the appalling treatment of staff who report serious incidents.
"We called for a helpline in December, February and May, so I am delighted that the First Minister has announced that there will be one."