A small number of soldiers manned roadblocks near the Murray Barracks in Port Moresby on Tuesday night, protesting a recruitment scandal that has already forced the nation's defence minister to step aside pending investigation.

Billy Joseph is accused of interfering with army recruitment, local media reported, enlisting soldiers from his home district in a process allegedly tainted by nepotism.

Believing they were unfairly targeted for blowing the whistle on the affair, a small core of soldiers have deserted their posts in protest against the government.

Chief of Defence Force Philip Polewara on Wednesday ordered all military units to implement "close camp" procedures for one month.

The security measures shut down weapons armouries, restrict the use of military vehicles and limit movements in and out of barracks.

"All unit commanders are to exercise strict command and control to ensure compliance," read a directive signed by Polewara and seen by AFP.

"Any breach of this directive will be treated as a serious disciplinary matter."

Prime Minister James Marape urged the troops to "immediately cease" their protest.

In a nod to their concerns, he said all soldiers who raised allegations through proper channels would be protected.

Police commissioner David Manning said any "troublemakers" would be "shut down and locked up".

Papua New Guinea signed a landmark mutual defence treaty with neighbour Australia in October.

The deal -- which is yet to be ratified in parliament -- was delayed over fears it would erode Papua New Guinea's sovereignty and non-aligned foreign policy.