Prime Minister Tony Abbott says his royal commission into unions, which will begin next month, is a "war on corruption" and not on trade unions themselves.

Governor-General Quentin Bryce has officially signed off on the terms of reference for the investigation.

It will largely focus on five unions, including the Health Services Union which was led by former Labor MP Craig Thomson.

Unions say the royal commission is a "political witch-hunt" by conservatives determined to weaken the Labor movement.

But Mr Abbott says that is not the case.

"Good unions have nothing to fear from this royal commission," he told Jon Faine on 774 ABC Melbourne this morning.

"This isn't declaring war on anyone. It's declaring war on wrongdoing. It's declaring war on corruption. It's declaring that there are certain standards in our society and whether you're a company official or a union official, you've got to obey the law."

Mr Abbott says a "good union" is "one where members' money is honestly administered and which is out there trying to ensure its members aren't oppressed".

He reiterated that he wanted the commission to report back by the end of the year.

"It's important we get to the bottom of this - we owe it to honest workers and honest unionists to ensure organisations are as clean as they can be," he said.

"The intent is to try and get a better system, the intent is to ensure we have honest unions.

"For too long, too many members of the Labor Party have been defending the indefensible."

Attorney-General George Brandis says the formal documents establishing the royal commission have been issued by the Governor-General.

Hearings will begin on April 9 and Justice Dyson Heydon is expected to report back by the end of 2014. However, the date can be extended if more time is requested.

Senator Brandis says he hopes Labor has nothing to fear from whatever the royal commission finds.

"If members of the Labor Party are fearful, that would only be because they have engaged in, or know about, misconduct," the Attorney-General said.

Senator Brandis says any suggestion of corruption within business would also be investigated by the royal commission.

The Attorney-General says a person of Justice Heydon’s eminence would not involve himself in a "political witch-hunt".

In announcing the commission last month, the Prime Minister said it would focus on five main unions, including the Health Services Union, once led by former Labor MP Craig Thomson.

Thomson was recently found guilty of fraud by using his HSU credit card to pay for prostitutes and to make cash withdrawals.

The Australian Workers Union, Transport Workers Union, Electrical Trades Union and the Construction Forestry Mining and Energy Union will also be under the microscope.

The commission has been charged with investigating the integrity of the financial management of unions, the accountability of officers and whether any unions have been used for any form of "unlawful purpose".

Labor and the unions want a police investigation to deal with allegations of corruption.