The probe will be part of a wider investigation that the watchdog has already announced into the Scottish Government's handling of Freedom of Information (FOI) requests. It follows claims last week that Mr Swinney sought to to withold details of corrspondence with Prince Charles over the Teach First charity.
That prompted a call from opposition politicians for the Deputy First Minister to be investigated. In a letter to Mr Scott, Information Commissioner Darren Fitzhenry has now confirmed he was already aware of the concerns surrounding the Deputy First Minister's office following correspondence with journalist and lecturer James McEnaney who was involved in a long-running FOI battle with the Scottish Government over the Teach First contacts.
Mr Fitzhenry's letter states: "I can therefore reassure you that I am aware of the cases you refer to; and indeed, as you point out in your letter, the documents were made available to Mr McEnaney after the involvement of my office in his appeal."
A row broke out last week after the emergence correspondence which suggested that Deputy First Minister was against releasing information concerning Prince Charles. The chain of emails also appeared to show FOI requests being screened by the government’s special advisers.
The involvement of special advisers, who have a political role in government, led to claims at Holyrood that the government was holding back information in case it proved politically embarrassing.
Mr Scott said: “The Information Commissioner is quite right to investigate these serious allegations.
"The documents reluctantly released by the Scottish Government suggested that special advisors were interfering in the content of replies to freedom of information requests in the very same week that ministers told me and Parliament they weren't.
"What ministers would 'prefer' isn't relevant when it comes to freedom of information. It is a matter of the law and the public’s right to information which is clearly defined in legislation.
"We need to see a thorough investigation of the Scottish Government's approach to information governance."