His comments follow government criticism of the Australian Broadcasting Corporation late last year after it broke a story about Australian spying on Indonesia, which sparked a major diplomatic crisis.
More recently, the conservative leader has been unhappy with ABC reports about asylum-seekers' claims they were tortured by the Australian navy during an operation at sea.
"It dismays Australians when the national broadcaster appears to take everyone's side but Australia's and I think it is a problem," he told commercial radio station 2GB.
The ABC, together with Guardian Australia, late last year ran allegations in leaked documents from US intelligence fugitive Snowden that Australia had spied on Indonesian President Susilo Bambang Yudhoyono and his wife in 2009.
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The premier also hit out at reporting of asylum-seeker claims that Australian sailors forced them to hold hot engine parts, burning their hands, as part of the government's military-led operation to stem the flow of boatpeople.
"If there's credible evidence, the ABC, like all other news organisations is entitled to report it, but ... You shouldn't leap to be critical of your own country," he said.
"You certainly ought to be prepared to give the Australian Navy and its hard-working personnel the benefit of the doubt," added Scott.
Asylum-seekers arriving on unauthorised boats in Australia, often via Indonesia, is a heated political issue and stopping them is a priority of the Abbott government.