The super-department was created against the advice of experts, agency bosses and even then-attorney-general George Brandis.

The polls say Bill Shorten is going to be prime minister in June and he will choose the person in charge of the Home Affairs department.

Whoever it is will control Australian Border Force, immigration, citizenship, ASIO, the Australian Federal Police, cybersecurity, multicultural affairs, transport security, countering extremism, and emergency management.

That's a lot.

The flaws of lumping all of those responsibilities into one department became clear in Senate estimates hearings this week.

It started with the case of Hakeem al-Araibi, the refugee footballer who escaped torture in Bahrain and was given protection in Australia.

He checked if he could leave the country to go to Thailand on his honeymoon and the AFP told him it was all good.

Except the ABF hadn't sent an email.

That email would have told the AFP that al-Araibi was under protection and Thailand should not be notified about a wrongly-issued Interpol red notice against him.

"It is clear that human error occurred within the ABF process," Australian Border Force boss Michael Outram told the Senate committee on Monday night.

One hand didn't know what the other was doing.

Then it was Paladin's turn.

A small company, handed a $423 million contract for security on Manus Island, with a complex history and not enough money in the bank to start work.

Home Affairs said they rushed ahead with the deal because no one else was willing to do it.

Whether there is something iffy with the deal or not, it's up to the AFP to investigate corruption in federal departments.

That's the same AFP that Home Affairs Minister Peter Dutton has responsibility for.

The AFP is also investigating who leaked a Home Affairs briefing document containing classified ASIO advice to The Australian newspaper.

The story about asylum-seeker medical transfers carried the headline: "Phelps bill a security threat: ASIO."

"The advice that ASIO gave was not what was represented on the front page of The Australian newspaper," ASIO director-general Duncan Lewis said.

The AFP will have to puzzle out just how that advice made its way out of the Home Affairs department in the middle of a highly contentious political debate.

This is part of the problem with combining all those powerful functions under one super-department.

One hand doesn't know what the other is doing, while a third hand has to investigate what the other hands are getting wrong.

Brandis used his final speech in parliament to have a subtle crack at Dutton for pushing previously separate public institutions under the same banner.

"To attack those institutions is to attack the rule of law itself," Brandis said at the time.

Labor will have a choice to make.

There is no obvious person to run Home Affairs.

"We've got several good people. We've got to win the election first," Shorten said this week.

Labor MPs have not traditionally viewed law and order jobs as a path to the leadership, unlike Liberal MPs, who have seen them as a chance to prove their conservative credentials.

That relieves some of the pressure on Shorten.

Labor could break up the department to remove some of the conflicting roles.

But the party is also wary of being accused of being soft on border protection.

"We want to maintain strong borders, we want to keep a role for Home Affairs but there are problems there aren't there?" Shorten said.

Budget cuts have also hit ABF and other sections. It is expensive to run the kind of border protection service Australia uses.

Solutions being considered include moving ASIO back into the Attorney-General's department, restoring some oversight of the domestic spy agency.

Perhaps the AFP could be moved out too, letting Home Affairs focus on immigration and border protection.

But if Labor wins next election, Shorten will have to decide whether breaking up the sprawling department is worth the pain he will take from the coalition over "weakening" border protection.

Australian Associated Press