The Federal Government will introduce legislation today to secure the future of hundreds of government programs possibly affected by a High Court ruling on its school chaplaincy program.

The High Court ruled last week that the program, set up by the Howard government and continued by Labor, exceeded the Commonwealth's funding powers.

Schools Minister Peter Garrett says without legislation, the next round of payments, due by close of business this Friday, cannot go ahead.

"$16.44 million, and that's owed - that will be owed to some 160 providers who employ chaplains and student welfare workers working in about 1,674 schools," he said.

"In terms of the largest single payments there, they go across the Scripture Union in Queensland, $5.7 million; to School's Ministries Group in South Australia, $2.6 million; Youth Care Western Australia, $2.5 (million); and Access Ministries in Victoria, $2.17 9 (million)."

Attorney-General Nicola Roxon says legislation will be introduced in Parliament today.

"But as part of that legislation, which will be in the form of amendments to the ... FMA (Financial Management and Accountability) Act, we are going to also include a range of other programs where there is not [a] legislative base that currently exists for them," she said.

Ms Roxon says the Government is taking a conservative approach and erring on the side of caution.

"The High Court has been quite clear that programs - even if supported by appropriations - need to have a legislative base or they need to fall into some other areas that were excluded by the court: payments to the states, of course individual payments like Centrelink payments and others, and a range of ordinary matters for government, so administrative payments etcetera," she said.

"So you will see tomorrow, and we will release tomorrow of course, when this is tabled, details of the other programs that will be included.

"They cover a vast range of areas and I can make absolutely clear that there is nothing in those regulations that are not programs that have already been approved by the Parliament through the Appropriations Act"

Ms Roxon estimates the legislation will validate between 5 to 10 per cent of all Commonwealth spending.

She warns the list may not be exhaustive, so if other programs need to be added to make them constitutional, that can be done later using regulations rather than legislation which can be disallowed by the Senate.

The Government has briefed the Opposition and Greens.

The Coalition says it will consider the legislation when it gets it, but has already declared it wants to ensure the chaplaincy program continues.

"Now I take some heart, I did see that Mr Pyne said, and I'm quoting him here, 'We will not use the High Court ruling to wipe out government programs'," Ms Roxon said.

"Senator Joyce has criticised the Greens saying that they shouldn't try and this is a quote, 'To bring down the whole show by blocking legislation'.

"So we take some heart that this is the sign, perhaps unusually, but would be welcome from the Government - from the Opposition and welcomed by the Government, if they were prepared to work sensibly on this, it's something that is in the interest of all Commonwealth governments of the future. And we hope that they will understand it is such."

The Greens too are waiting to see the draft bill, adding they want to ensure parliamentary scrutiny of government programs as required by the High Court, is guaranteed.

But they will seek to change the chaplains program so that all student support officers are properly qualified.