The pair were caught after being cornered by police in Banana Court. One was apprehended at the scene and the other suspect was picked up after fleeing the scene.
Police are currently preparing charges against the youngsters, who are both under 16, and they are expected to appear before the Juvenile Crime Prevention Committee soon.
They are suspected of being responsible for a string of attempted burglaries around Avarua that evening, during which several of the MFEM offices were damaged.
It is believed they had gone through several rooms of the government department, causing significant damage. Police said: “The building was subjected to ransacking throughout the office areas”.
It is unclear if the workings of the department will be affected by the break-in, or if files and other documents have been lost.
A spokeswoman for Cook Islands Investment Corporation, which was also targeted, said the damage in their offices had been minimal and they had been able to continue working. However, she added that the department would be looking at ways of improving security.
Police were called just before dawn on Tuesday morning when the pair were spotted by a member of the public inside the Banana Court complex.
A police spokesman said the pair were being interviewed “in connection with burglary and other unlawful activity”.
The arrests come a week after fears were raised over the behaviour of youths congregating in nearby Taputapuatea and break-ins at the Empire Cinema, where a fire was started, and other nearby offices.
Police would not say if the events on Tuesday morning were related to those earlier incidents.