Police have come under fire for leaving hundreds of Malaysia Airlines passengers trapped on the tarmac for 90 minutes after a bomb scare forced the flight to return to Melbourne.

Flight MH128 was forced to return to Melbourne after a man allegedly brandishing a device, which he claimed to be a bomb, threatened to blow up the flight shortly after take off.

And while the accused man, 25-year-old Sri Lankan student Manodh Marks, was overpowered by passengers and crew, and the flight landed at 11.43pm, police did not storm the aircraft until 1.21am. 

Chief Commissioner Graham Ashton defended the actions of police, saying there were concerns there may have been accomplices and bombs on the plane.

"If there had been a device on board, if we had offloaded people immediately without properly going through the process ... we could have had a very serious mass casualty incident on our hands," Mr Ashton told a parliamentary hearing on Thursday.

"You are damned if you do, damned if you don't in these situations, and they [commanders] always have got to make a judgement call when you've got that many lives in their hands."

The incident comes just a week after the Lindt cafe siege coronial inquiry found that police needed to act quicker.

Mr Ashton said there was "no delay" in this case. "There was no lack of response, there was no delay in response," he said.

He said he had assessed a full chronology of the event and was "not seeing any time gaps or delays that were problematic".

"We certainly appreciate that when you are on a plane in a situation, one minute can seem like an hour, it can seem like an interminable wait," he said.

However, a police source said the responding officers had been poorly briefed and believed for up to an hour that the suspect may have been carrying an explosive device.

It is also understood they had not been told where the man was being restrained when they stormed the plane.

Mr Marks refused to appear in Melbourne Magistrates Court on Thursday, with the court hearing he would need urgent mental health help.

He faces two federal aviation charges of recklessly endangering the safety of an aircraft and threatening to destroy, damage or endanger the safety of an aircraft, or kill or injure anyone on board. The charges carry a potential penalty of 10 years.

Mr Marks left a psychiatric unit at Monash Health on Wednesday before buying a ticket for MH128.

The Australian Federal Police said it worked closely with Victoria Police to examine multiple and conflicting sources of information received via social media and official sources. 

"At all times the safety and security of the passengers and crew was the primary focus for police," an AFP statement said. 

After Victoria Police was called, it took about 30 minutes for the special operations group to arrive, and nearly an hour before they stormed the plane.

Officers responding to the crisis were further held up, after being unable to locate firearms and body armour, the source said.

The extraordinary delay raises troubling questions about staffing at Melbourne Airport and an apparent failure to plan for such an incident. 

The critical incident response team head arrived at 12.23am, and the special operations group two minutes later.

Premier Daniel Andrews backed the police response. "The police have to know exactly what they are dealing with before they gain entry to the plane and potentially make a bad situation much, much worse," Mr Andrews said. 

But Opposition Leader Matthew Guy said with eight exits on board and the suspect "hog tied" authorities should have been able to evacuate the plane more quickly.

"We need to know why did it take so long to get these people off this plane," Mr Guy said.

"It has taken 80 minutes, if there was a bomb on board and it is full of fuel and there is 200 passengers that [evacuation] needs to be done very, very quickly."

Mr Guy, who had not been briefed, also called for an independent inquiry. 

Some passengers claimed they were told by airline staff it would only be 10 minutes after landing before police took the man from the plane, and they would be allowed to leave.

The man had been subdued within minutes of making the threat, and the device he was grasping was soon found to be benign.

Passengers on board, however, remained on edge, with some involved in containing the man.

Other passengers were not told what had occurred until after police boarded the plane.

John Coyne, a senior analyst specialising in border security at the Australian Strategic Policy Institute, said many of the issues raised in the Lindt cafe siege inquest would have been playing out. 

"It's the difference between going into a quick action operation – which is when something bad is continuing to happen – or taking a more deliberate approach," Dr Coyne said. 

"No one was getting hurt and my understanding is that there had been a visual check of this football-shaped device and it didn't look like a bomb.

"The situation was under control, the passenger was restrained and had no access to the device." 

Dr Coyne said the authorities responded appropriately given those factors, with the alternative being to board the plane immediately after landing, potentially with officers less suited to the situation than Victoria Police's special operations group. 

with Patrick Hatch and Ebony Bowden