The former finance secretary Kate Forbes expressed surprise to the inquiry that minutes were not kept for some meetings.
The UK government has also been criticised over its record-keeping, with the Scottish secretary Alister Jack telling the inquiry he had deleted all of his messages to create memory space on his phone.
The Scottish government stated that it remained “committed” to ensuring “openness and transparency” and that Scotland had the most “open and far-reaching” FOI legislation in the UK.
A spokesman said: “We have not yet received the notice from the Scottish Information Commissioner, when we do so we will respond and of course cooperate with the commissioner as required.
“The first minister has commissioned an externally led review into the use of mobile messaging apps and non-corporate technology in the Scottish government. This will take particular account of government interaction with statutory public inquiries.”
The commissioner is the appeal body for FOI requests made to Scottish public authorities.