During First Minister’s Questions, Labour’s Rhoda Grant said: “The First Minister appears to be aware that her government and their special advisers are holding back material from FOIs that could cause them embarrassment.
“Does she therefore believe that saving their own blushes is more important than transparency, and indeed, the law?”
The First Minister said she had previously been questioned on information based on a FOI request, which she would not have been able to do if “we were withholding it in some way”.
She added: “FOI requests are handled by Scottish Government officials, they seek comments from relevant parts of the Scottish Government and consider whether Ministerial clearance should be sought.
“That’s entirely appropriate because the legal duty to comply with FOI legislation lies with Scottish Ministers.”
She said FOI requests are handled in line with the legislation at all times.
Ms Grant earlier lodged an Urgent Question on the issue but it was not selected.
Her party colleague Neil Findlay later raised a point of order in which he claimed special advisers are “routinely copied into and politically interfering in replies” to FOI emails.
He also claimed Deputy First Minister John Swinney was “caught ordering key documents to be withdrawn”.
He asked Presiding Officer Ken Macintosh if he had been informed when an independent review of the Scottish Government’s FOI performance, backed by parliament last year, will take place.
Mr Macintosh said Mr Findlay’s intervention was not a point of order.
Earlier, the Conservatives called for the parliamentary business minister to answer questions at Holyrood.
Conservative MSP Edward Mountain said Joe Fitzpatrick may have misled parliament when questioned on the issue last summer.
It follows research by lecturer and journalist James McEnaney which suggested that documents were removed from an FOI release at the request of Mr Swinney and his special adviser.
When asked in June whether requests were being screened for potential political damage by special advisers, Mr Fitzpatrick responded: “No, requests are all prepared by Scottish Government officials.
“Special advisers have a role in assessing draft responses for accuracy.”
Mr Mountain said: “We now know that the answers given by Mr Fitzpatrick to the Scottish Parliament are not true.
“The evidence suggests that special advisers are routinely involved in the freedom of information process for political purposes and John Swinney himself is suppressing documents when it suits him.
“Mr Fitzpatrick categorically denied this on the floor of the Scottish Parliament.
“Joe Fitzpatrick must return to the Scottish Parliament immediately and explain these responses.
“It appears this may well be a breach of the Ministerial Code of Conduct. It is entirely unethical for a Scottish minister to mislead the Scottish Parliament.”