The new probe centres around allegations that Fife Council staff inappropriately accessed confidential social work files on the toddler whose "killer mum", Rosdeep Adekayo, is serving an 11-year sentence for culpable homicide.
"Police Scotland is currently investigating some specific matters concerning data management within Fife Council," a spokesperson said.
A significant case review is also underway into Mikaeel's death which will involve looking into all files into the toddler's case after it was found that his death could have been avoided if agencies had properly supervised his drug addict mother.
She then reported him missing, triggering a massive search operation which ultimately ended in her arrest earlier this year.
The shattered father of the boy, estranged from his mother for a few years, spoke in his first-ever interview recently about fears that the murder was the result of Adekayo's hatred for him.
Zahid Saeed, a chef who now lives with his wife and two daughters in Fife, Scotland, described Adekayo as a "controlling manipulator" who could not bear that their son was growing into a spitting image of his father.
The 30-year-old says he regrets a three-month fling which had resulted in Mikaeel's birth and not forcing Adekayo into allowing access to his son.
"I was helpless. She refused to put me on the birth certificate so I had no parental rights," he said.
It has now emerged that Rosdeep is being allowed prison visits by Mikaeel's twin sister and her three other siblings from another father.
The 34-year-old avoided a murder trial and the possibility of a life sentence of up to 35 years after a court accepted her guilty plea to the lesser charge of culpable homicide.
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