The Australian Tax Office has decided against publishing the names of employers registered to pay the backpacker tax.

A ministerial submission by the ATO released to the Uniting Church under Freedom of Information laws says "employer registration information will not be displayed on the Australian Business Register ABN lookup tool".

Under the Treasury Laws Amendment (Working Holiday Maker Reform) Bill 2016, which has not yet been debated, employers of working holiday makers are required to register with the ATO and confirm what rate they could expect to be taxed.

When it introduced the bill, the federal government said backpackers would be able to look up employers via ABN Lookup, making the register publicly accessible.

Mark Zirnsak, director of justice with the Uniting Church Synod of Victoria and Tasmania said the Federal Government should stick to its original promise to let backpackers know which employers have registered to pay the correct tax.

"Backpackers suffer as a result of being exploited and the community suffers due to loss of tax revenue to fund things like schools, hospitals, mental health services and aged care," Mr Zirnsak said.

"It is completely unacceptable for the ATO to act as if the government has gotten its secrecy law for the employers of backpackers through the parliament.

"The government should abandon its secrecy bill and ask the ATO to implement a proper public register of those employers of backpackers who are doing the right thing on wages and taxes."

Labor MP Andrew Leigh, the Shadow Assistant Treasurer, wrote to the Commissioner of Taxation Chris Jordan to ask if the Treasurer had advised the ATO not to publish the employer register as originally proposed.

In his reply to Mr Leigh, Mr Jordan said at this point in time he has "chosen not to make an employer's working holiday maker registration publicly available".

He said he had the discretion "to make certain information publicly available".

A spokesman for the ATO said as the Registrar of the Australian Business Register (ABR), the Commissioner was "exercising his discretion not to make an employer's working holiday maker registration publicly available".

Mr Leigh said Australia needed transparency to reduce the exploitation of vulnerable workers, "but the government is creating the opposite".

"This has been a fiasco from the beginning, when the so-called "Backpacker Tax" first appeared in 2015. The government is denying working holiday makers something they promised, a public register that allows for visa holders to review who is registered for the program," Mr Leigh said.

"The government can send a clear signal to the Tax Commissioner by immediately removing this dodgy policy from the notice paper.

"Australia has some of the greatest attractions in the world for young globetrotters - our workplace laws should be among them."

A spokesman for the Treasurer Scott Morrison said the bill was proposed by Senator Leyonhjelm.

"The government agreed to introduce the amendment after reaching an agreement with the senator to pass the original WYHM legislation. The government will honour its commitment," the spokesman said.

"This commitment did not extend to the successful passage of the amendment.

"The government is committed to protecting the rights of backpackers and protecting them from exploitation.

"We provided additional funding to the ATO and FWO to assist with ongoing compliance initiatives and to address exploitation of working holiday makers."