THE Australian Greens want the national school chaplaincy program replaced with a scheme that provides students with tertiary-qualified counsellors.

The program was placed in jeopardy last week after the High Court declared the way it was funded exceeded the Commonwealth's power.

But on Tuesday the House of Representatives rushed through a bill to validate payments for the program.

Another 427 grants and programs, worth billions of dollars, are also covered by the legislation.

On Wednesday, Greens Senator Penny Wright called for the program to be replaced so that "genuine counselling and assistance" could be given to students.

Such a scheme would ensure counsellors with tertiary qualifications could deal with contemporary pressures faced by students.

"We know from surveys young people are finding life increasingly difficult to negotiate," she told reporters in Canberra.

The Greens will on Wednesday seek to amend the Financial Framework Legislation Amendment Bill, during a second reading in the Senate.