* Australia confirms "multiple breaches" but gives no details
* Relations between Australia and Indonesia at their lowest since 1990s
* Significant trade ties between often uneasy neighbours
* Australian opposition leader blasts secrecy (Updates with)
By Matt Siegel and Jane Wardell
SYDNEY, Jan 17 (Reuters) - Australia apologised to Indonesia on Friday for naval breaches of Indonesian territory as part of Canberra's controversial policy of stopping boats carrying would-be asylum seekers from entering its waters.
Acknowledgement of the breaches will likely further strain ties that had already hit their lowest point since the 1990s after recent allegations Australia had spied on President Susilo Bambang Yudhoyono and other senior Indonesian officials.
Australian Immigration Minister Scott Morrison said he had been told earlier this week about the "inadvertent breaches" on multiple days and immediately informed the Indonesian navy.
He said Foreign Minister Julie Bishop was unable to reach her Indonesian counterpart, Marty Natalegawa, who is in Myanmar for a meeting of the Association of Southeast Asian Nations, to discuss the breaches and that a formal apology would be issued by Australia's embassy in Jakarta on Friday.
Indonesia downgraded its relations with Australia in November as a result of the spying allegations, suspending intelligence and military cooperation, including over asylum seekers.
A protracted crisis between the often uneasy neighbours could have serious repercussions. Indonesia is a major importer of Australian agricultural products such as wheat and live cattle. Australia is Indonesia's 10th-largest export market.
Morrison's office did not reply to queries about whether the formal apology had been issued, but said Bishop had sent a letter to Natalegawa. Officials in Jakarta had no immediate comment, but a Defence Ministry press conference was scheduled for the afternoon.
Morrison said on Friday Australia "deeply regrets" the breaches of territorial sovereignty but at the same time maintained Australia's right to protect its own borders.
"We have offered the apologies, we have been very clear about what has occurred both with Indonesia and here today," he told reporters.
"But we won't let this setback get in the way of the job we were elected to do, which is stop the boats," he said.
The number of refugees reaching Australia pales in comparison with other countries but it is a polarising political issue that also stokes tension with Indonesia over border policies that have been criticised by the United Nations and international human rights groups.
Prime Minister Tony Abbott's conservative government came to power partly because of its tough campaign against asylum seekers after an easing of border policies by the former Labor government that resulted in a rise in the number of boats.
Its policies include offshore detention centres that hold thousands of asylum seekers, many of whom have fled conflicts in Afghanistan, Darfur, Pakistan, Somalia and Syria.
CONCERNS OVER SECRECY
Abbott's government is also coming under fire at home over the secrecy surrounding its "Operation Sovereign Borders" asylum policy, which he recently likened to a war. He has said secrecy is important to prevent "the enemy" receiving information.
On Wednesday, Morrison moved to restrict access to information further even as he touted the operation's success, refusing to confirm reports that the navy had forced the return of a number of boats to Indonesia in recent weeks.
The U.N. refugee agency has asked for information from the government, warning that Australia could be breaking international law if it is forcing boats back to Indonesia without proper regard for refugees' safety.
Australian opposition leader Bill Shorten said that the government's lack of transparency was adding to the growing mistrust between Australia and Indonesia.
"And now what we see is that they're going to try to blame the navy for implementing Abbot government policies, which are causing more problems than they're solving," he told reporters in Sydney.
Graeme McGregor, a spokesman for Amnesty International, called "absurd" the government's continued refusal to provide greater information about the policy to the public in the wake of an incursion that he says threatens to derail the regional framework on refugee resettlement.
"I'm not entirely clear what purpose that secrecy serves, except to deny accountability around these policies," he told Reuters.
"I think the public have a right to know how their money is being spent, and I think the current government's policies of secrecy and masking that information are not helpful."
Lieutenant General Angus Campbell, the officer in charge of the operation, said the breaches occurred on multiple days by "a vessel or vessels" but declined to give more details.
Many of those trying to reach Australia pay people-smugglers in Indonesia to make the perilous journey in often unsafe boats.
Last year's spying allegations left relations between the two countries at their lowest level since 1999, when Australia sent troops into East Timor amid escalating violence after Indonesia pulled its troops out of its former colony. (Editing by Nick Macfie)