The Scottish Information Commissioner was asked to serve four separate formal information notices to the Scottish Government to gain access to information withheld by ministers.
This is a rare step for the transparency watchdog to take, with most information sharing connected to appeals being probed by the commissioner done on an informal basis.
Critics said this showed the Scottish Government was treating transparency with “contempt” and accused it of having a culture that was “rotten to the core”.
It is understood this information, which the commissioner must view to be able to judge whether it was lawfully withheld from the public, covers James Hamilton’s report into whether Nicola Sturgeon breached the ministerial code.
It also covers the internal decision report, which has never been published, of the Government’s botched investigation into harassment complaints against former first minister Mr Salmond.
Two other probes being looked at by the commissioner are also covered by these information notices. It is understood this covers the same sensitive information.
Scottish Conservative MSP Murdo Fraser, who was a member of the Holyrood committee that investigated the botched harassment complaints investigation, said the request from ministers was “extraordinary”.
He said: “At every turn during the inquiry, SNP ministers failed to be transparent and it appears that approach hasn’t changed one bit.
“It is extraordinary that the commissioner has been put in this position simply to get information from the SNP Government.
“They clearly think that they can just ignore these requests and brush issues under the carpet.
“It is time for them to urgently co-operate and stop treating the idea of transparency with such contempt.”
Jackie Baillie, Scottish Labour’s deputy leader who was also a member of the committee, said this was another example of the Government’s “web of secrecy and cover-up”.
She said: “Time after time, the Government did all it could to keep vital information from the committee.
"Transparency and openness are vital to democracy, but this Government has turned its back on that.
"Frankly, the culture of the Scottish Government is rotten to the core.”
Alex Cole-Hamilton, Scottish Liberal Democrat leader and member of the harassment complaints committee, said Nicola Sturgeon must make it clear to her officials to “co-operate in full” with the information commissioner.
He said: “I know from the role that I played sitting on the Salmond Inquiry that trying to get evidence out of the Government was like pulling teeth, so it doesn't surprise me in the slightest that the Government are once again facing being hauled over the coals over their approach to information transparency.
"This is a highly unusual step for the information commissioner to take and reflects the seriousness of both the matters under discussion and the obstacles that journalists and campaigners have faced in trying to get to the bottom of this sorry affair.”
A Government spokesperson said: “We will continue to engage constructively with the Scottish Information Commissioner around these cases, which contain particularly sensitive information, to ensure that we comply fully with our obligations.”