"This is a giant leap into the abyss. Here's hoping we don't kill the golden goose," said the federation's president, Don Nicolson, after the announcement that New Zealand First and the Greens were backing the bill.
He said politicians seemed to have forgotten that agriculture was laying New Zealand's golden egg.
"What we have is a whole lot of gamesmanship that is divorced from the real world," Mr Nicolson said.
"While it may provide some politicians with a very short-term fix, the risks will be felt by farmers and other New Zealanders for decades."
Mr Nicolson said it was "extremely disappointing" that the bill would now be passed by Parliament.
"The federation will remain steadfast in its determination to get some common sense and practical solutions to the mess that this legislation now creates," he said.
"If there is a bright side, it's not obvious right now."
Federation representatives met NZ First MPs today to put their case, hoping to hold off an agreement that would give the Government a majority on the bill.
The talks began at 4pm. Unknown to the federation team, NZ First announced at 4.15pm that it was backing the bill.