Federal Labor has warned the loss of Indonesian cooperation will be a significant setback to tackling people smuggling.
Jakarta has pulled the plug on all military co-operation in retaliation for the Abbott's government's refusal to explain spying allegations.
Navy patrols combating people smugglers will be withdrawn.
Senior Labor MP Tony Burke, a former immigration minister, says Indonesian cooperation had built up over time.
"It's not just like you can turn it on and off," he told Sky News on Thursday.
"If we lose the cooperation there, it's not like the day cooperation resumes, it's right back from where we were."
Mr Burke insisted the Abbott government had Labor's full backing for efforts to resolve the diplomatic row with Indonesia.
Australian Greens leader Christine Milne warned Indonesia's decision could endanger lives.
"You have to wonder what's going to happen with the lives of refugees," she told reporters in Canberra.
She urged Prime Minister Tony Abbott to stop jeopardising Australia's relationship with Indonesia simply to win votes at home.
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