The civil servant "workstreams" focus on every aspect of creating a new state, from security policy to welfare.
The SNP Government has been under severe pressure recently over how an independent Scotland would function.
The First Minister was criticised for his explanation of a separate Scotland's relationship with the European Union. His answers on currency and defence have also been scrutinised.
Now the Scottish Government has promised to lay out the nuts and bolts of independence in a White Paper ahead of the 2014 referendum.
However, Better Together, the campaign to keep Scotland in the UK, said Alex Salmond was using publicly funded mandarins to "justify his separatist dream".
Ministers set up a series of working groups last November, the results of which will feed into the White Paper.
The Government confirmed after request under Freedom of Information legislation that civil servants are working on 16 independence-related projects. Titles include "external affairs", likely to cover EU membership, "public finances and macroeconomic policy", "business and enterprise" and the "structure and capacity of government".
Other workstreams have been created on health, welfare and defence and security.
On the projects' remits, the Scottish Government gave a stock response that applied to 15 of them, saying it was "work showing how Scotland would make the transition to a successful, independent country following a yes vote for independence".
A separate remit related to the "referendum bill" workstream.
Deputy First Minister Nicola Sturgeon said: "Following the Edinburgh agreement, the basic process and legality of the referendum has been settled and it is now time to step up the work of explaining to the voters of Scotland the opportunities that independence will deliver.
"I am clear that over the next two years the Scottish Government has three clear responsibilities: To set out clearly our proposals for the architecture of an independent Scotland; to hear and answer people's questions about the transition to independence; and to set out the opportunities that being independent can bring."
It emerged last month that the UK Government had established 13 workstreams of its own to set out the benefits of Scotland staying in the UK.
Topics include Scotland's economic performance, financial services and banking, and debt and borrowing. Papers on each will be published next year.
A spokesman for Better Together said: "Alex Salmond has, it would seem, hundreds of publicy-funded civil servants working to find reasons to justify his separatist dream.
"People in Scotland know better. They know that ripping up our country makes no sense."
Scottish Labour MSP Patricia Ferguson said: "Alex Salmond still can't answer the basic questions of how a separate Scotland would work."
l Scotland would have to pay more to borrow money as an independent country than it currently does as part of the UK, Michael Moore, the Scottish Secretary, will tell business leaders at CBI Scotland today.