Sixty thousand sheep destined for live export to Kuwait will remain in Australia indefinitely, after the suspension of a second licence belonging to the embattled Emanuel Exports.

The dramatic midnight intervention came after Fairfax Media revealed the owners of Emanuel Exports had applied to ship the Merino wethers despite having their main licence to export suspended.

An investigation into alleged historical breaches of animal welfare standards is ongoing. The suspension was triggered by - although does not directly involve - the horrific footage that emerged in April showing thousands of sheep dying en route to the Middle East on the Awassi Express in 2017.

Just days after the suspension, Nicholas Daws took over from his father Graham Daws as sole director of their live export companies, in what sources said was an attempt to present a fresh face to the embattled company and increase their prospects of being granted a permit to export the sheep to the Middle East.