Rows between rival electoral commissioners had led to physical fights, Jecha Salum Jecha said.
The opposition says the vote on the islands was cancelled because it won.
The main challenger in the national presidential election, Edward Lowassa, said the problems in Zanzibar could be mirrored across the country.
Earlier, he called for the national electoral commission to stop releasing results, alleging the whole process nationwide had been marred by fraud.
The elections in Tanzania are the most competitive in the country’s history, with four opposition parties forming the Ukawa coalition to challenge the ruling CCM’s 54-year grip on power.
Previous elections have turned violent on semi-autonomous Zanzibar, whose two main islands are Unguja, often referred to as Zanzibar, and Pemba.
Mr Lowassa urged his supporters to remain calm and not to engage in street protests.
‘Agents ejected from polling stations’
In his statement, Mr Jecha accused Zanzibari electoral commissioners of being partisan.
More votes had been cast in some areas than the registered number of voters, especially in Pemba, where some party agents had been ejected from polling stations, Mr Jecha said.
The ballot papers for the national presidential election have been taken to Tanzania’s main city Dar es Salaam, where they will continue to be counted.
It is unclear if and when new elections for Zanzibar’s president and parliament will be held.