Nicola Sturgeon has failed to explicitly deny using a "private or party" email account for Scottish Government business.
The First Minister's statement was in reply to a question from Tory MSP Donald Cameron during First Minister's Questions.
A spokesman later said Ms Sturgeon does not use a personal account to "conduct substantive Government business".
Party email accounts are not usually covered by freedom of information legislation, meaning messages would not necessarily be available to members of the public.
The First Minister 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."
The question came after concerns were raised over the lack of rules in place to limit the practice.
Speaking to the Times on Thursday, Transparency International UK research manager Steve Goodrich said guidance should be issued to MSPs on best practice to ensure information is available to the public when requested.
The Times reported the First Minister did not send a single email to ministers using their Government accounts in June and only sent two notes to special advisers - both of which came from a party email account.
Following FMQs, a spokesman for the First Minister said: "The First Minister doesn't use her personal email account to conduct substantive Government business.
"The simple fact is quite often members of the public will email her at these email addresses and she will then forward said email from her account."
He added: "Members of the public will frequently email her at her personal accounts about any number of things, some of which may relate to Government business, some may relate to constituency business, some may relate to party business."But if
it relates to Government business, the First Minister will then forward said email to her private office and it then is within Government, and if it's taken forward in any substantial sense in terms of Government policy, it will have a formal status within Government and be subject to all the usual rules of Government."
Asked whether any Government ministers use private emails to conduct Government business, the spokesman said: "Ministers don't conduct Government business by private email accounts, they simply don't."
Mr Cameron said: "The First Minister failed to answer a simple yes-no question today. It simply isn't good enough.
"Surely everyone can agree that using private emails to conduct Government business is wrong.
"If it has happened, it only begs the question as to what the First Minister has to hide."
He added: "The SNP Government already has a desperate record when it comes to transparency.
"I hope the First Minister will do the right thing and make her position clear over the coming days."