Australia's live export industry is in shock after Indonesia has drastically reduced the number of import permits for cattle for the current quarter.
The allocation for the July to September quarter is just 50,000, which is significantly less than the 200,000 permits that were expected and the 250,000 for the quarter just gone.
Australian Livestock Exporters' Council chief executive Alison Penfold described the news as a "disappointment" and a "surprise".
She told ABC 24 on Tuesday that the reasons for the decision, which was made late last week, had not yet been made clear.
But she said they would be due to trade and food security - and not any other issues going on with the Australia-Indonesia relationship.
"It certainly will present some challenges, particularly around shipping for the industry but we've been trading with Indonesia now for over 30 years," she said of the decision.
"We have had our ups and downs but we will continue to work constructively with our customers and within the parameters that are set for the trade."
A spokesman for Agriculture Minister Barnaby Joyce said the government would continue to "make representations on behalf of exporters to ensure this important trade relationship is maintained".
He is expected to address the media from Perth later on Tuesday.
Mr Shorten told reporters that he was "most concerned" about what was happening to cattle exports.
"This is a grave concern."
When pressed about the reasons behind the dramatic cut in permits, he said: "I sincerely hope that our relationship with Indonesia at the political level is not driving this reduction."
The opposition's agriculture spokesman Joel Fitzgibbon argued the relationship was certainly a factor.
"Of course the Abbott government's relationship with Indonesia or the deterioration of it won't be helping at all," he told the ABC.
In a statement, he also said, "there's no doubt Australia's relationship with Indonesia has deteriorated under Tony Abbott".
Labor also pointed to Mr Joyce's split with cabinet over the government's approval of an Shenhua coal mine in his electorate.
"The situation in Indonesia is a shocking development but should not have been entirely unexpected if Minister Joyce was across his brief and not distracted by his internal wars with cabinet," Mr Fitzgibbon said.
The former Labor government faced a diplomatic storm over cattle of its own, when it banned live exports to Indonesia in 2011.
It suddenly stopped exports after footage emerged of animal cruelty in Indonesia, sparking outrage from both the Australian cattle industry and Australia's neighbour.
The cattle permit change comes just weeks after former Indonesian foreign minister Marty Natalegawa said relations between Australia and Indonesia appeared to be at their lowest point.
Australia's Ambassador to Indonesia, Paul Grigson, has only recently resumed his post in Jakarta. He was briefly recalled after Andrew Chan and Myuran Sukumaran were executed.
Relations between Indonesia and Australia have also been tested over the past 18 months by allegations that Australian spies tapped former president Susilo Bambang Yudhoyono's phone during Labor's time in office, as well as the Abbott government's asylum seeker boat turnbacks policy.