Almost 2,000 people canceled their e-vote with a paper ballot at the local elections last week.
In Estonian elections, it is possible for a voter to cast a ballot more than once both online and on paper, but if this occurs only the paper ballot is counted.
Voters can also cast multiple votes online with only the final one counting. There were 23,600 repeat voters this year.
This election saw a record-high turnout for e-voting with 47 percent of voters - almost 274,000 people - choosing to cast a ballot online. At the last local election in 2017, the rate was 32 percent and at the previous election eight years ago it was 21 percent.
The popularity of e-voting is different around the country. The highest online turnout was 57 percent on the western island of Hiiu County but it fell to 35 percent in the eastern county of Ida-Viru.
Vote counts continue on Tuesday to double-check the result. On Monday, e-votes were recounted.
Arne Koitmäe, the head of the State Electoral Service, said previous experience has shown that this does not affect the general election result.
The election results will not be officially announced for several weeks until after all issues have been resolved.
Editor: Helen Wright