The scutiny process, which proceeds the vote count, follows on from the end of polling in the autonomous Papua New Guinea region's non-binding referendum.
After polling closed on Saturday, officials with the Bougainville Referendum Commission have gathered all 249 ballot boxes at the count centre in Buka.
The Chief Referendum Officer Mauricio Claudio said that as of Sunday afternoon, 103 boxes had been verified, with about 80 officials overseeing the overall process in eight-hour shifts.
"The count centre is now operational and humming away at a smooth, methodical pace. This work is on track with our modelling, and teams are working well, safeguarding the legality and of course the accuracy of the count."
The referendum result is expected to be announced before the end of the week.
He said that over the next few days all 249 bllot boxes would be opened "with verification of seals and materials against Referendum Journal - already completed and checked by Presiding Officers and Assistant Returning Officers at the regional centres".
"Only after we are absolutely sure that we have the correct number of used, unused and spoilt ballot papers will mixing of all ballot papers take place and the counting begins. This is best international practice to ensure the secrecy of votes.
"We're satisfied with the progress of the count, the accuracy, the smoothness and the ownership shown by the media, the scrutineers and the observers," Mr Claudio said.
"We're confident that we have a sound process in place which will soon, within days, bring the Bougainville referendum to a successful conclusion."