The head of Australia's chief intelligence organisation has intervened in the high stakes political stoush over border security and says his agency's classified advice on the medical evacuations bill has been misrepresented.

Australian Security Intelligence Organisation boss Duncan Lewis repudiated a front page report in The Australian - relied on by the government as evidence the bill would undermine border security - accusing the newspaper of misrepresenting ASIO advice.

Director-general of security Duncan Lewis said ASIO's advice had been misrepresented. Credit:Dominic Lorrimer

He said the agency's advice was confined to the bill's invocation of the ASIO Act, rather than more general advice about the border security implications of the proposal.

"The advice that ASIO gave was not what was represented on the front page of The Australian newspaper," Mr Lewis told a Senate inquiry.