A Somali-born university student charged with plotting a New Year's Eve terrorist attack failed to appear in court because there wasn't enough room for him on a prison bus.

Ali Khalif Shire Ali, 21, had connections to jihadist circles when he is alleged by police to have planned a shooting spree at Melbourne's Federation Square to mark the start of 2017.

The African Muslim from Werribee, in the city's west, was due to face a preliminary hearing at Melbourne Magistrates Court on Monday to decide if he should stand trial.

A Somali-born university student charged with plotting a New Year's Eve terrorist attack failed to appear in court because there wasn't enough room for him on a prison bus

The court was told, however, that Corrections Victoria didn't have enough room on a prison bus for him to be taken to court, the Herald Sun reported.

Magistrate Simon Zebrowski described the situation as the 'most extraordinary thing'.

In another logistical stuff-up, the holding cells in the courthouse were also full.

'He's not even here yet, and there's no room in the cells for him,' the magistrate said.

Mr Zebrowksi told the court Mr Ali's absence meant the case could not be heard.

His case was adjourned until Tuesday, but it is likely, if Mr Ali appears, to be closed to the public as undercover Australian Federal Police detectives are called as witnesses.

Ali Khalif Shire Ali, 21, had connections to jihadist circles when he is alleged to have planned a shooting spree at Melbourne's Federation Square to mark the start of 2017