The new probe was launched after 18 babies died in their first 28 days of life in March, causing the mortality rate to breach a set threshold.
It is the second time this limit has been reached since records began in 2017, after 21 deaths were reported in September, sparking another investigation.
The cause is not babies having Covid, she said, but it may be related to complications in pregnant women who have the disease, or pressures on healthcare as a result of the pandemic.
The increase in deaths is "absolutely not” related to the Covid vaccine, she said, as this has been shown to be safe in pregnancy.
"The other thing are the wider impacts of Covid-19 on healthcare services and that is something that needs to be thought about as well.
"Maternity and neonatal services are stretched and continue to feel the effects of Covid on staffing.
"But we can't forget that it might be other causes altogether, so it's really important that we investigate.
"It is very unusual to see these outliers, and understanding why is going to be crucial."
A spokesperson for Public Health Scotland said: "Each of the losses reflected in the information reported is a tragedy for those involved.
"The review processes to identify and mitigate any contributing factors are being led by the responsible agencies, and are ongoing.
"Public Health Scotland will continue to monitor data on neonatal health outcomes to inform and support this work.”
The Scottish Government confirmed investigations are underway.
“We are working with PHS, the Scottish National Neonatal Network and the Maternity and Children Quality Improvement Collaborative to understand any possible contributing factors to ensure we continue to improve the care of the smallest and sickest babies in Scotland,” a spokesperson said.