Minister for Agriculture Barnaby Joyce rues the previous Labor administration's "dopey" live cattle ban that has left the current government facing a farmers' class action.
Northern Territory farmers and businesses launched action this week for compensation over losses resulting from the 2011 ban.
The Nationals MP would not comment on how costly the Federal Court action could be, but said it has put the government in a difficult position.
"I wish we'd never been left with this dilemma on our hands by the previous government," Mr Joyce said in Canberra on Wednesday.
Mr Joyce suggested the ban was detrimental to Australia's long-term trade relationship with Indonesia, which looks for security and longevity in trade agreements.
"It was not only a dopey decision on an agricultural basis," he said.
"(But) on a bilateral relations basis."
Almost two dozen Northern Territory businesses have filed for compensation over losses incurred after the Labor government suspended live cattle exports.
The ban was lifted a month after it was introduced.
Indonesia subsequently introduced import quotas in an effort to lift the country's self-sufficiency, cutting Australian beef imports by 75 per cent.
Labor's agriculture spokesman Joel Fitzgibbon has praised the Gillard government's changes to animal welfare procedures, but said it could have worked with the industry earlier on for a better result.
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