It emerged the First Minister's office destroys her handwritten notes, rendering them unobtainable by Freedom of Information (FoI) requests.
However, Ms Sturgeon explained the notes are typed up into emails, which she said were "fully open to FoI legislation" and denied it was done to avoid the content of her memos being seen.
Asked about the report in The Times on a campaign visit to Aberdeen South, Ms Sturgeon said: "Just to be very clear here, when I write a handwritten note on a government submission, what happens is that my private office transcribes that note into an email that is then retained within the government in electronic form and fully open to FoI legislation.
"There is absolutely nothing different to what's happened previously or untoward in any way, and I think opposition parties should stop trying to suggest otherwise."
The policy has been in place since Jack McConnell was First Minister, Ms Sturgeon said.
She added: "I've not changed it in any way, I haven't introduced any new policies, my predecessors as first minister used exactly the same system, so I think other parties are trying to cast aspersions where there is no justification for doing so."
She added: "If I write a handwritten note, my private office transcribes that note into an email. Otherwise, how would the policy official know what instruction I was giving on a government submission?
"That's how the system works, it's how I have dealt with government papers ever since I was in government in 2007 and, as we know, that policy has been in place since 2004-05, so my immediate predecessors as first ministers used the same system and any insinuation - and I think it is an insinuation - that somehow I have changed the rules or created a system to try to evade scrutiny has absolutely no substance whatsoever."
The Scottish Conservatives have officially reported Ms Sturgeon and her staff for actions which they say also include using a party political SNP email account to direct civil servants and conduct government business.
MSP Donald Cameron has urged the National Records of Scotland to intervene and investigate the First Minister for potentially breaching the Public Records (Scotland) Act 2011.
In a letter to the NRS he said that the Scottish Government may have broken section 1 of the Act by circumventing their own Records Management Plan, rendering it redundant, and by failing to keep records that should be retained for at least five years.
He also called for Paul Lowe, the Keeper of the Records, to urgently step in to investigate the practices.
"By using a party email account and destroying hand written instructions, Nicola Sturgeon's government is putting every imaginable hurdle in the way to limit transparency and keep her decisions secret," he said. .
“This is an unacceptable and unprecedented attempt to avoid scrutiny and it simply cannot be allowed to continue any longer.
“That's why I've written to the Keeper of the Records today to ask that he investigates this as a matter of urgency.
“Even for this SNP government, with its dubious record on transparency, this is a new low. It cannot be considered business as usual to treat the historical record of government at will, and it raises the very serious question – what does Nicola Sturgeon have to hide?”
The Scottish Government has said the First Minister has complied with the law.
Under the legislation, the Keeper of the Records of Scotland can carry out a review of public bodies, to ensure records are being correctly kept.
The First Minister has previously come under fire for her alleged use of an SNP email address for government business, which is not subject to Freedom of Information legislation and where content can be freely deleted - unlike official government accounts.
When challenged on the matter of using an SNP email in Holyrood in October, Ms Sturgeon said she conducts the majority of government business on paper. At the time she said: "The government is completely subject to freedom of information legislation and we would be covered by any of that.
"Most of the way I, rightly or wrongly, conduct government business is on paper. I receive paper boxes not email boxes and I do handwritten notes. That's the way I conduct business.
"We will continue to respond to freedom of information requests on any particular issue."
Mr Cameron added: "This is bizarre and potentially unlawful behaviour It appears the First Minister sends handwritten notes to her officials. Those officials then send emails to the Civil Service.
“Then her handwritten notes are destroyed. It reeks of secrecy and paranoia.”
The current policy for handling notes was brought into force in 2004 and the Scottish Government has said there has been no change to the regulation since.
The government has said that the First Minister's office did not retain handwritten notes, and any "handwritten notes received by the First Minister's private office are articulated to officials via email. It is made clear that any emails and attachments relating to a decision, request or comment made by a minister must be filed appropriately by the relevant policy areas."
Guidance from the NRS says it should only accept duplicates of official records if what is being offered "is in effect a primary set of records and similar duplicates of equal value are being preserved in other archives." or the originals have been destroyed in "exceptional circumstances", such as a fire.
A spokesman for the Scottish Government said: “From 2004/05 onwards it was agreed that responses from ministers are relayed by ministerial offices to the relevant policy teams who are responsible for maintaining the official record.
“It is not the responsibility of ministerial offices to keep the official record. The Scottish Government is confident we comply with all records management requirements.
“The Scottish Government’s records management policy is submitted to the Keeper of the Records and is reviewed annually, or sooner if changes to the law require it, as set out under the Public Records (Scotland) Act 2011.
“The Scottish Government has an agreement with the National Records of Scotland regarding the transmission of documents for the archive, which includes support for the transfer of electronic records.”