More than $1,000 was taken from the courthouse after the back door was pried open, along with a bottle of alcohol that was left as evidence from a trial, said Sgt. Dale McLeod.
He said evidence is typically stored in the courthouse for about a month.
Neither sheriff Morgan Schindel nor deputy justice minister Markus Weber would say whether the courthouse plans to improve security to prevent future break-ins.
"We can't comment," said Weber.
Police continue to investigate other unresolved break-ins in Iqaluit, including one where carved walrus tusks were stolen from the museum.