Nicola Sturgeon said she had had a very rare reaction to the H1N1 virus.
Sharon Pentleton, 26, who is critically ill, was taken to Crosshouse Hospital, in Kilmarnock, last week, where she had been put on a ventilator.
She was transferred to Stockholm on Thursday because no beds were available in the UK for the procedure she needed.
Ms Pentleton, from North Ayrshire, needs a procedure in which her blood will be circulated out of her body and oxygen added artificially.
It is known as extra corporeal membrane oxygenation (ECMO) and involves a machine taking over the function of the patient's heart and lungs.
The UK has a national ECMO unit in Leicester, to which Scottish patients would normally be sent.However, all five beds in the unit were in use.
Before Ms Pentleton was transferred, a medical team from Sweden came to Scotland to assess her. She was then accompanied by the Swedish doctors on a private flight from Prestwick in Ayrshire.
Ms Sturgeon told BBC Scotland: "She is now getting treatment that gives her the best possible chance of survival."
She said doctors were pleased with how the pregnant woman had coped with the journey and she said the treatment "might and hopefully will save her life".
She added: "It is a highly-specialised procedure and that is why given a bed was found for her in Sweden the decision was taken by her clinical team to recommend transfer there."
Family hopes
A family statement, issued through NHS Ayrshire and Arran, went on: "We are grateful for the care and support we have received from intensive care staff at Crosshouse Hospital and, of course, to the medical care team who travelled from Sweden to start the specialist treatment that we hope will make her well.
"Sharon continues to receive the best possible treatment but is still gravely ill.
"For this reason we will not be making any further statement and we would ask that we are left alone to concentrate on Sharon."
Dr Palle Palmer, from Karolinska University Hospital in Stockholm, told the BBC the treatment would take pressure off the patient's lungs.
"We buy some time for the lungs to get better . . . but she has to get better by herself," he said.
Patient swaps
He added it was common for patients to be transferred to Sweden from other countries and they also sent patients abroad for this procedure.
"We have been swapping patients for 10 years.
"We send about 10 patients per year out and bring in 10-15 patients."
Dr Robert Masterton, executive medical director of NHS Ayrshire and Arran said: "Once an ECMO bed was identified in Sweden, our intensive care specialists worked closely with our Swedish colleagues to make sure the patient was stable before being transferred."
He added: "The family have been fully involved in this decision and support this referral. They have asked for privacy while they concentrate on the patient's treatment and recovery."
The health secretary stressed this particular case was unusual.
Ms Sturgeon said: "It remains the case that for the overwhelming majority of people who get this virus the symptoms are very mild and they will make a full recovery within a matter of days without any complications whatsoever."
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