Memory sticks containing election tallies and boxes of hand-counted ballots were being delivered to a secure location in Augusta.
The state's top election officials said the office may release unofficial election results sometime next week after additional tabulations.
With the ranked-choice voting system, voters casting ballots rank the candidate preferences from first to last. A candidate who collects a majority of the vote wins. If there is no majority, the last-place candidate is eliminated and votes reallocated. The process is repeated until there is a majority winner.
The voting system is used in 11 local jurisdictions. It was used for the first time in a statewide primary on Tuesday in Maine.
Maine residents also voted Tuesday to retain the system, nullifying a legislative delay and allowing it to be used in November federal elections.
Ranked-choice voting is sometimes referred to as an "instant runoff" because there's no need for a runoff election.
But the process is far from instant in Maine. Couriers had to travel to more than 500 locations - from far northern Maine to islands off the coast - to retrieve the ballots from municipal clerks.
The schedule of the couriers was kept secret to avoid public meddling.
In some cases, schedules were kept secret from clerks as well. In Westbrook, Deputy Clerk Angela Holmes expected the courier Friday, but a driver showed up late Thursday morning instead.
Mike Israelson, vice president of General Courier, said the process was going smoothly overall with 80 pickups within in the first hour or two. It's expected to take two days to retrieve all of the ballots, state officials said.
In the Democratic primary, additional tabulations are required in the gubernatorial and Maine's 2nd Congressional District race.
Attorney General Janet Mills had the most first-place votes for governor, and state Rep. Jared Golden, a Marine veteran, had the most for the congressional seat.
For now, ranked-choice voting cannot be used in state general elections, including this November's gubernatorial election because of state constitutional concerns.
Supporters of the new voting system plan to push a constitutional amendment that would allow it to be used in the governors' race, where nine out of the last 11 elections failed to produce a majority winner. Republicans oppose the proposal.
Associated Press writers David Sharp in Portland and Patrick Whittle in Westbrook contributed to this report.
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