Immigration head Martin Bowles has defended his department amid allegations of widespread visa fraud, saying he is investigating a leak of internal documents.

Fairfax newspapers have reported departmental documents show fraud relating to 90 per cent of skilled migration visas, stemming back to 2008.

Afghan visa applications are alleged to have a similar rate of suspected fraud, and there are concerns about criminal and national security implications.

Mr Bowles, the Secretary of the Immigration Department, says the allegations are serious and call into question the integrity of Australia's migration and visa programs.

"These allegations, including that migration fraud is going undetected and is not being appropriately investigated, are of great concern to me," he said in a statement.

The leaked immigration files showed repeated warnings that visa fraud and migration crime was widespread due to the collapse of the department's investigation and enforcement capacity.

Mr Bowles says the Immigration Department is doing its utmost to combat fraud, but he says this is a "challenging space" and people will always try to thwart the system and enter Australia on a fraudulent basis.

"There is rigour in the department’s processes but there is also always room to improve," he said.

The Department head says there will be an investigation into the leak of internal documents to journalists.

"I am looking into this as not only is it against the APS Code of Conduct and entirely inappropriate, such documents taken in isolation are not reflective of the full picture."

Mr Bowles also says some of the material which has been published is out of date.

"Some of the documents and reports which were obtained by members of the media through Freedom of Information are several years old and do not reflect the work the department has done since those reports were published and is currently doing to combat fraud."

Mr Bowles said the overwhelming majority of people who travelled or migrated to Australia did so lawfully.

"When the department receives information suggesting otherwise, it acts on it," he said.

Scott Morrison says allegations pre-date the Abbott Government

Immigration Minister Scott Morrison says the allegations are serious, but appear to relate to Labor's time in office.

Martin Bowles and Mr Morrison have both pointed to significant changes in the management of Australia's borders since the Abbott Government came to power, such as the establishment of the Australia Border Force in May.

Mr Morrison said the Government had increased the number of field visits by about 20 per cent, particularly for 457 visa integrity compliance.

"That has resulted in an increased number of warnings and various other cases taken forward," he told Fairfax radio.

The organisation representing migration agents says new regulations brought in 12 months ago have toughened penalties for visa fraud.

"There are very strict migration regulations now that go to the identity of the person providing false and misleading documentation," said Angela Chan from the Institute of Migration Agents.

"To the point that if people do this, they can be refused a visa. Or if they have been granted a visa, they can have their residence cancelled."

Former Labor immigration minister Chris Bowen said every immigration system had to deal with fraud.

"We weren't the first government to deal with immigration fraud and we won't be the last," he told reporters in Cairns.

Mr Bowen, now shadow treasurer, said Labor did all it could.

"We absolutely, in office, did not reduce resources to this. In fact, quite the contrary," he said.

"[The Labor] government ... implemented biometric testing, which is testing to make sure the people who were applying for a visa are the actual people they are claiming to be."

The new allegations do not relate to asylum seekers who arrived by boat, an issue which has been the focus of the Government's secretive Operation Sovereign Borders effort.

But Mr Morrison denied boats were a distraction for the department.

"Almost 1,200 people died at sea as a result of [arriving by boat], so you can deal with stopping the boats as well as dealing with these visa integrity issues," he said.

Mr Morrison said ensuring the integrity of the skilled migration program was as important as stopping asylum seeker boats.

"It's an important program for Australia, to have proper, skilled migration to Australia through a process with integrity, so people can come the right way and don't rort it," he said.

"I'm as serious about that as I am about stopping the boats."