The box was taken to the town hall for counting around one hour later than other boxes.
Manchester City Council's deputy returning officer insisted there was no evidence of malpractice and the officer took the ballot box home to finish paperwork.
The late box was used in the election for Cheetham, a ward in which Manchester City Council's deputy leader Martin Pagel (Lab) was expected to score heavily.
But deputy returning officer Andrew Scallan said no seals on the box had been broken and the 'integrity' of the election was not in doubt.
In a letter to the candidates he wrote: 'The presiding officer was taken aback by the volume [of paperwork] he had to complete and had not followed the instructions to prepare as much as possible during the day.
'[He] did not realise the impact [his actions] would have on the count. He has apologised unreservedly for his actions.'
Mr Afzal, who reported the matter, said the election should be made 'null and void'.
A greater Manchester police spokeswoman confirmed they are investigating a number of matters in connection with the Cheetham election.