A Singapore Airlines flight from Melbourne to Wellington was cancelled on Saturday after the pilot failed a drug and alcohol test.
The Australian Civil Aviation Authority screened the crew as part of their random drug and alcohol screening programme as they were carrying out their pre-flight checks.
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Singapore Airlines spokesperson Karl Schubert said the pilot has returned to Singapore.
"The pilot in question was stood down and has been suspended from all duties effective immediately. He has returned to Singapore where a full investigation will be undertaken," he said.
@M_iikun on Twitter said they missed the All Blacks test against South Africa as a result.
"Care to try to explain why your captain (ie most experienced person on the aircraft) of SQ247 waits until boarding time to decide they're too ill/drunk to fly?" he posted.
"Will miss the 1st #allblacks #rugby match I bought tickets for and flew to WLG from NRT to see #sad."
The return flight from Wellington to Singapore via Melbourne was also cancelled as a result.
The airline has since apologised and said safety is its highest priority. Passengers affected have been contacted by Singapore Airlines to make alternative arrangements.
Singapore Airlines' Melbourne-Wellington route was only launched in May this year. The new service is operated by a Boeing 777-200.