Mistakes made may have led to deaths, injuries and increased risk, the agency claims.
The agency has investigated roughly 50 reports countrywide, cases in which the ambulance took too long to arrive or failed to show up at all.
Some of the cases have led to further injuries for the patient, while others put the injured or ill at risk.
According to the agency, the reasons behind the flaws are communication problems and, in some cases, failure to locate the correct address.
In one of the cases reviewed, 23-year-old Emil Linnell died in his Stockholm apartment, after repeatedly having phoned for an ambulance.
According to the agency, the telephone operator didn't follow the prepared check-list meant to aid the on-call nurse to ask the correct questions.
On top of this, SOS Alarm's routines for cooperation didn't work. The doctor, supposed to be available for emergency medical assessment, wasn't contacted.
Instead the emergency operator contacted a different doctor altogether, according to the agency.
Linnell subsequently died of a burst spleen.
The agency now demands that SOS Alarm ensure that all employees are given the correct training, and that the routines for cooperation between different professions and caregivers function properly.
SOS Alarm is to present them with a report of the changes made to their operations, latest by January 15th.
If the demands are not met, SOS Alarm can be made to pay a fine, the agency said in a statement.
In total, the agency have investigated 52 cases, but have thus far reached a formal decision in only one of the cases, that of 23-year-old Linell.
Because of this, Maria Carlund, investigator at the National Board of Health and Welfare, didn't want to go into details about the other cases.
How other patients have been endangered or injured is not yet information available to the public.
"But there have been several severe cases," said Carlund to news agency TT.
In the Stockholm case, the nurse at SOS Alarm didn't follow the instructions he had been given. But the board also identified flaws in SOS Alarm's organisation.
"There's a shared responsibility, and we've found fault with both. We've opened a separate case for investigating the circumstances around the nurse," said Carlund.
SOS Alarm were unwilling to comment on the National Board of Health and Welfare's decision on Friday.
"We have to look into this, and won't be commenting until Monday," said Anders Klarström, press spokesman at SOS Alarm, to TT.
Following the death of 23 year-old Linell in April, the nurse who took his call was charged with involuntary manslaughter.
According to the prosecutor, the nurse did not follow SOS Alarm's protocol. The trial is set to begin on Monday in the Stockholm District Court.