The Environmental Protection Authority (EPA) Bill was passed into law last night on a vote of 63 to 59, with the Maori Party and United Future's Peter Dunne backing the Government.
The EPA has been National Party policy since 2006 and was introduced in a preliminary form after the 2008 election.
The bill formally establishes it as an independent Crown entity from July 1 this year.
The Maori Party wanted a Treaty clause put into it, which the Government agreed to.
But ACT's deputy leader, John Boscawen, said the deal was done behind closed doors.
"The National-ACT confidence and supply agreement clearly states that National will operate a `no surprises' policy with ACT and yet we only heard of the amendment last Thursday after it was tabled," he said.
"This is something ACT was not consulted on."
Mr Boscawen said ACT told National on April 12 it would support the bill, and it didn't need the Maori Party's support or the Treaty clause to hold a majority vote on it.
Instead, the Maori Party was now claiming it as a triumph, he said.
The clause requires the Treaty to be recognised by the authority, a common requirement in new legislation.
Labour's Charles Chauvel said there were now four different Treaty clauses in different items of environment legislation and the situation was a mess.
