The Department of Prime Minister and Cabinet paid $1.3 million through recruitment firms to the company at the centre of what is allegedly one of the largest tax frauds in Australian history, a Senate estimates committee has heard.

On Tuesday night, the committee was warned of a government-wide payroll exposure to Plutus, the company that allegedly defrauded the Tax Office of $165 million in just 11 months, after a directive from the Department of Finance for all government agencies to check their books.

The committee heard the Department of Prime Minister and Cabinet had 11 information and communications technology contractors paid through the company allegedly run by Adam Cranston, the son of the Australian Taxation Office Deputy Commissioner Michael Cranston.

"During the course of the day we have confirmed the number that we now understand have been affected are 11," said the department's chief financial officer, Charlotte Tressler.