The figures prompted Labour to accuse the Government of an "obsession with secrecy" while the Government insisted that it was seeking to legislate to improve the system.
The first annual report of new Commissioner, Rosemary Agnew, shows that her office received 524 appeals in 2011-12, up by 100 on the previous year, a rise of almost 24%. Within that increased total the proportion of appeals relating to the Scottish Government or its agencies rose from 15% to 28%.
Labour's Paul Martin said: "The fact that the number of complaints from members of the public about the SNP Government has almost doubled in a year is symptomatic of the SNP's obsession with secrecy."
He added: "The Freedom of Information Act is a pillar of our democracy and the SNP is treating it with utter contempt."
Ms Agnew told MSPs last week an estimated 15,000 families had lost the right to FoI their landlord because of the shift from councils to housing associations.
She said: "It is simply not acceptable that citizens' rights continue to be eroded through complex changes in the delivery of services."
The Commissioner told The Herald the trends were probably a mixture of the decline in the number of bodies responding under arms-length arrangements and growing public knowledge of the right to appeal to her office.
A Scottish Government spokesperson said: "We are currently progressing an FOI Bill through parliament which will improve the system and make more information available to the public earlier."