According to documents obtained by The Scottish Sun, the meetings were held on November 24, 2021, January 14 and February 3, 2022.
They discussed the “approach to the development and delivery” of a new prospectus for independence as well as what “topics” to include in the document.
However, officials refused to provide further details, claiming it could “impact the formulation of government policy”.
Over the weekend, the First Minister admitted there is still no date for a Holyrood Bill for a second independence referendum.
“I haven't decided on the specific date for that right now,” said Ms Sturgeon, as she maintained she was keeping to her plan to have Indyref2 in 2023.
The First Minister has said she wants a referendum by the end of 2023, dependent on the Covid situation, with the hopes of Scotland then becoming independent in 2026.
However, Boris Johnson has refused to grant Holyrood the power it needs to hold a legally watertight vote, creating a constitutional impasse.
Ms Sturgeon has said she will pass a Referendum Bill at Holyrood regardless, however that would require prior sign-off by the Lord Advocate Dorothy Bain.
In March, Patrick Harvie, the Scottish Green's co-leader, said the bill would be tabled in Holyrood "before too long".
The former SNP media boss Kevin Pringle recently conceded a new vote was “unlikely to take place” in 2023 “given the hurdles to be overcome and extensive preparations required”.
However speaking to Scotland on Sunday, Ms Sturgeon said Mr Pringle was “wrong” and she would carry on as she originally intended, based on the SNP’s Holyrood win last year.
She said: “I've set out the timetable I'm working to. Nothing has changed around that. Plans for that are underway, so nothing has changed.
“I won the mandate for that in an election this time last year."
Reacting to the documents, Pamela Nash, chief executive of Scotland in Union, said: “Nicola Sturgeon and her ministers are increasingly out of touch with the people of Scotland.
“Amid a cost-of-living crisis and pressure on local public services, the last thing the government should be focused on is how to divide Scotland once again.
“Taking up civil service time and resources like this is irresponsible and inappropriate. The entire focus of government should be on bringing people and communities together.
“At the forthcoming local elections, voters can choose candidates who prioritise local services rather than SNP councillors who are only interested in an unwanted and divisive second referendum.
“As part of the UK we can ensure Scotland’s best days are ahead of us by investing more in local services, protecting jobs and livelihoods, and bringing communities together.”