Federal authorities confirmed on Thursday that an investigation is underway on alleged security loopholes in Darwin's immigration facilities following the lapses that occurred last month, which was punctuated by a peaceful protest of detained immigrants who sprung out from the centre.

An Immigration Department spokesman admitted that the Northern Territory Licensing Commission is conducting an inquiry on Serco, which was tasked by the department to provide for security on the detention facilities.

The same official told AAP that Serco is delegating some of its responsibilities to MSS Security though he stressed that the Immigration Department has ensured that the security firm was duly reminded to only employ trained and licensed personnel and comply with all relevant laws.

The spokesman also revealed that some former MSS Security employees were facing compliance actions and Serco has been cooperative so far with the ongoing investigation, which came following series of incidents in the past few months where asylum seekers rioted in the facilities, vandalised the centre and staged a protest action after breaking out of detention.

Meanwhile, federal opposition immigration spokesman Scott Morrison warned that the government would be made responsible if allegations of unlicensed workers were made to man the immigration centre were proven true.

Mr Morrison told ABC that the government cannot put the entire blame on security contractors since it has the ultimate responsibility as he stressed that "the government must ensure that that licensed operators are only ever used in the care and supervision of people who are being detained by the state."