Chief executive Lin Homer suspended elections officer John Owen - a noted expert in election administration - and a colleague after a member of staff tipped off Liberal Democrat group leader John Hemming about the crate.
He visited the office concerned accompanied by police and the council's chief legal officer Mirza Ahmad and found the postal votes on top of a cupboard.
Ms Homer said: 'Certain evidence has been handed over to the police and I have started an investigation into the matter.
A judge overturned last June's results in two Birmingham wards and made scathing criticisms of the security of postal voting (LGC, 7 April).
Malcolm Dumper, executive director of the Association of Electoral Administrators, said: 'John Owen is highly regarded - he has been running the largest elections office in the country. I hope he is exonerated.'
The council has written to all 53,000 postal voters to verify their request is genuine.