Opposition Leader Bill Shorten says the government needs to stop blaming the navy and take responsibility for its own border protection policy.
Immigration Minister Scott Morrison revealed on Friday that Australian navy vessels entered Indonesian waters without official permission, despite previous assurances by him and Prime Minister Tony Abbott that such incursions would never happen.
The incidents were blamed on inadvertent "positional errors" made by navy crews.
"This is incredibly serious," Mr Shorten said in a statement on Friday.
Mr Morrison learned of the incident on Wednesday, just hours after he had told reporters at a media conference that vessels involved in Operation Sovereign Borders "have never and will never violate the sovereign territory of another country".
Mr Shorten said it was "poor form" for Mr Morrison to blame the navy for his failings.
"These service men and women do an extremely tough job under very difficult circumstances and they shouldn't be blamed for the failings of the Abbott government and its policies," Mr Shorten said.
"He should start taking responsibility for his own policies that resulted in an incident like this occurring."
Mr Shorten said a strong and constructive relationship with Indonesia was fundamental to Australia's national interest and this was now being put at risk.
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