Australia's biggest banks say they have been forced to sign a confidentiality agreement before the Government provides executives with draft details of a new $6.2 billion tax.

Banking executives are furious having already criticised the Government for the surprise budget hit, saying Treasury set an unreasonably short deadline for submissions.

Many executives have already indicated they will pass the costs of the levy to customers and shareholders, arguing they cannot absorb the tax as the Government claims they should.

Australian Bankers' Association chief executive Anna Bligh said the banks were shocked by the gag clause, claiming it would prevent consultation with shareholders and board members.

"A bad tax has now become a secret tax," Ms Bligh said in a statement.

"The Government is going to extraordinary lengths to keep this tax hidden from the people who will be most affected by it and from the public.

"A totally unacceptable public policy process has today gone from bad to worse."

Treasurer Scott Morrison has pleaded with banks not to pass the cost of a new tax on to customers, telling executives the public "already don't like you very much".

Despite enjoying bipartisan support, the levy has been slammed as a "very bad idea" by David Murray, the head of the Government's financial system inquiry.

In a statement, Mr Morrison said the order would not stop banking executives from sharing the information within their office, with board members or with commercial advisors.

"The major banks have made individual submissions to the Government and we are respecting requests made for confidentiality of the submissions, including any subsequent comments they may provide," Mr Morrison said.

Many of the banks have published their submissions online claiming the levy has been hastily designed and should be lifted once the budget returns to surplus.

"The non-disclosure arrangements used in this case are not an irregular practice for governments when consulting with commercial entities over draft legislation, and have been used recently by the Turnbull Government for the multinational anti-avoidance laws and the diverted profits tax," Mr Morrison said.