Healthcare Improvement Scotland have been commissioned to lead a review into the neonatal death rates.
It follows the higher than expected deaths in both March 2022 and September last year, as published by Public Health Scotland.
At least 18 babies under four weeks old died in March – a rate of 4.6 per 1,000 births.
The wider inquiry is understood to have been triggered because the mortality rate passed an "upper control" threshold of 4.4 per 1,000 births.
The average mortality rate among newborns is just over two per 1,000 births.
The review will cover all reported deaths across Scotland between April 1, 2021 and March 31, 2022 to find out if there is anything that may have contributed to the increase.
Anything identified will feed into recommendations and actions to improve the quality of care for mothers and babies.
The Scottish Government said the investigation is expected to take no longer than six to nine months once the review team is formed.
Public health minister Maree Todd said: “Every death is a tragedy for the families involved. That is why earlier this year I committed to this review to find out if there is a reason for the increase.
“I appreciate how difficult this time is for anyone affected and I would encourage them to access support if they wish to do so. There is information about organisations and help available on the National Bereavement Care Pathways Scotland as well as the Scottish Government website.”
Neonatal mortality is defined as the death of a baby within four weeks of birth.
The review will not duplicate any matters which are, or have been, the subject of other review, investigation or audit processes.
Dr Sarah Stock, an expert in maternal and foetal medicine at the University of Edinburgh, told a national newspaper earlier this year: "I think the numbers are really troubling and I don't think we know the reasons why yet.
"What we do know it's not neonatal Covid – the rates of Covid-19 infection in babies are very low and deaths from Covid are thankfully very, very small, so this isn't Covid affecting babies."