Lewisham Labour Party members had already chosen former council leader Steve Bullock as its candidate over current leader David Sullivan by a 63-vote margin.
But the result was rejected by supporters of Mr Sullivan who say some voters had received multiple ballots and ballot papers had been sent to dead party members.
Investigations by the Greater London Labour Party revealed there were some 200 people on its list who were ineligible to vote.
Labour Party general secretary David Triesman wrote personally to apologise to the candidates. In the letter he said: 'The party owes an apology to members in Lewisham, not least the candidates.'
Mr Sullivan said he was confident local party members would understand the reasons for having to re-run the ballot.
The mayoral elections are due to take place in May.