In an interview with the Financial Times, Fry accused the BBC of reproducing content from local newspapers with "little added work".
He also attacked local council newsletters such as Tower Hamlets' East End Life as "contributing significantly" to the challenges faced by local newspaper publishers.
Local newspapers are among the most affected by the downturn as they are heavily reliant on local property and employment advertising.
This morning, DMGT, which owns the Daily Mail, reported an 18% decline in revenues in its regional news division Northcliffe Media.
Fry, who joined Johnston Press from Archant in January, also called for a relaxation on merger restrictions and for the "regulators of this industry to come into the 21st Century".
He said: "The Office of Fair Trading has yet to be convinced that we are in competition as local papers with the print edition of Autotrader, let alone the online edition.
"They don't accept that local papers in London are in competition with the Standard [Evening Standard] and they haven't even begun to think about whether Rightmove is a competitor."
Fry's comments come just days after KPMG was appointed to the company in a "preparatory role" in advance of the company renewing its debt agreements later in the year.
New Johnston Press exec hits out at BBC and council-funded papers
Newly appointed Johnston Press chief executive John Fry has hit out at council-funded local newspapers and the BBC as damaging to the local newspaper sector.
