Murkowski waged a write-in campaign after losing the Republican nomination to Miller in August. She has 92,164 votes, but that total includes 7,601 write-in votes that have been challenged by the Miller campaign.
Miller has 90,458 votes.
Besides the ballots being counted, as many as 600 more from overseas and military addresses could be submitted by a deadline Wednesday. The state plans to count those by Friday.
Miller has filed a federal lawsuit seeking to have the state follow election law, which calls for write-in ballots to have the oval filled in and the last name of the candidate or the name as it appears on the declaration of candidacy. In the Senate race, it would be "Murkowski" or "Lisa Murkowski." The state has been using discretion in determining voter intent, allowing minor misspellings and pointing to prior case law as justification.
Murkowski's camp has said Miller is seeking to disenfranchise thousands of voters who made an effort to write in her name but had trouble doing so.
Miller observers have challenged the 7,601 write-in votes for misspellings, illegibility, extra words or oddly filled-in ovals.
Some of those ballots included mangled or hard-to-read lettering, but also entries like "Murkowski, Lisa," and "Lisa Murkowski Republican." Another 1,869 ballots have been challenged and not counted by the state. Many had Murkowski's name written in, but included a blank oval. Murkowski observers objected to the decision.