Australia's foreign spies will soon have new powers to better assist the Defence Force in its military operations against Islamic State in Iraq.

The Senate on Wednesday passed legislation which also allows Australian Federal Police to issue control orders for people suspected of supporting or facilitating foreign fighters.

Labor backed the bill after the government agreed to 16 minor amendments of a bipartisan parliamentary committee.

The amendments provide more clarity on how a "foreign fighter" is defined and how anti-terrorism control orders work.

The new laws enable the Australian Secret Intelligence Service to conduct counter-terrorism activities in Iraq without having to wait for written approval by a senior minister.

It also changes the means by which the foreign minister, who is responsible for ASIS, authorises the agency to undertake activities relating to a "class of Australian persons" rather than individuals.

The Australian Greens opposed the bill after failing to push through changes that would restrict control orders.

Control orders allow police to detain suspects without charge.

But Attorney-General George Brandis said the orders were not about punishment but preventing terrorist attacks.

"We're talking about terrorism here. We're talking about the destruction of lives, the destruction of property," he told parliament.

"Once the conduct has occurred, it's too late."

The Greens also wanted to legislate against ASIS using torture, but Senator Brandis said claims that violence could be used were "completely wrong".

The bill simply legislated co-operation that already existed between Defence and ASIS, he said.

Liberal Democrat David Leyonhjelm also opposed the bill, claiming there was no evidence that new powers were needed.

He believes they may have a "seriously chilling" effect on free speech and could be misused by future governments.

Senator Leyonhjelm is concerned that broad definitions of "supporting or facilitating" foreign fighters mean police will not be able to determine who is a real threat.

The bill is the third bipartisan counter-terrorism bill to go before the Senate in recent months. A fourth that mandates the collection of metadata is expected in early 2015.

The bill now goes to the House of Representatives, where passage is assured.