It is not clear if the government was aware non-government schools and Australia's 37 public universities were among the charities formally registered with the Australian Charities and Not-For-Profits Commission.

But on Monday afternoon it was clarified universities and schools would not be eligible for the 15 per cent threshold,which Assistant Minister for Charities Zed Seselja said was targeted at organisations like the Salvation Army.

"This supports charities that are expected to have a significant increase in demand for their services,"he said.

"Non-government schools and universities are eligible for the JobKeeper Payment. However,they will need to meet the turnover threshold of 30 per cent for those with an annual turnover of less than $1 billion."

Ms Jackson said the sector was"disappointed to have been excluded"from the arrangements and would continue discussions with the government about possible support for universities.

"As not-for-profit charities,we welcomed the Treasurer’s announcement about amendments to JobKeeper that would have seen most universities included. It would have backed our ability to reduce job losses,"she said.

Vicki Thomson,chief executive of the Group of Eight universities,had embraced the initial announcement and said Mr Frydenberg had been"unambiguous"the lower threshold would apply to all registered charities.

"And that includes our universities who operate on a not for profit basis – and we expect government to follow through on that basis ... not shift the ground rules in less than a day,"she said.

Luke Sheehy,executive director of the Australian Technology Network of Universities,said:"It would be very disappointing if the government casts universities adrift given the important role we're playing finding solutions to this crisis as well as the role we'll play in the recovery."

Labor education spokeswoman Tanya Plibersek said schools and universities were registered charities"so they should be covered by the government’s special JobKeeper arrangements".

"It would be a big mistake for the government to abandon universities and schools during this crisis,"she said.