Australia’s attorney general, George Brandis, appears to have granted the country’s domestic spy agency access to journalists’ metadata in a small number of cases, the agency’s head has revealed.

Duncan Lewis, the director-general of the Australian Security Intelligence Agency (Asio), confirmed in parliament on Tuesday that the agency had been granted some journalist information warrants.

Independent senator Nick Xenophon has been pursuing Asio over the details of the warrants, and focused repeated questioning on Lewis in Senate estimates on Tuesday.

They warrants came into force in October 2015 in part to secure passage of Australia’s sweeping data retention laws that require telecommunications companies to store phone and web metadata for two years.

The changes now require law enforcement to obtain warrants from a judge if they are seeking access to a journalist’s phone or web metadata. But Asio is not required to go to a judge, and must instead approach the attorney general directly to obtain a journalist information warrant.

After facing repeated questioning from Xenophon about why he could not specify the number of warrants, Lewis said: “I can answer that very promptly. The number is small. Because of the small nature of the number ... it would be very easy to start identifying who and what cases were involved. So I’m just not prepared to go to the issue of numbers where it will clearly ... it could clearly point to an investigation that is underway.”

Xenophon said he was “not asking you to break down how many were from Newscorp, or Fairfax or the Guardian”.

“I just want to know how many journalist information warrants have been issued.”

Lewis said: “I cannot and I will not in a public setting provide the number of investigations into a class of person ... The numbers as I said are small and a simple exercise in deduction would start to throw light on the investigations that are currently underway.”

It is the first time Asio has confirmed that it obtained access to journalists’ phone or web records. The Australian federal police has confirmed to date that it has not sought a journalist information warrant since they were introduced.

But it has previously confirmed accessing journalists’ phone records prior to the introduction of the warrants in order to pursue whistleblowers who disclosed government information.

While the AFP has generally sought information for the purposes of investigating leaks of commonwealth information, the nature of Asio’s investigations remain opaque.

Lewis told Xenophon the agency had provided details in the agency’s classified report, which is available only to the parliamentary joint committee on intelligence and security. “In the classified report there is something of an answer to your question, but I am not prepared to discuss it in this environment,” he said.