Tanzania's elections were thrown into doubt Wednesday after the semi-autonomous Zanzibar archipelago annulled polls, sparking tension on the islands and raising questions about national presidential results due Thursday.

Opposition parties have also alleged rigging in Sunday's presidential, general and local elections, the tightest polls ever in the East African nation, with the governing party facing the first major challenge to its dominance in decades.

Zanzibar's electoral commission on Wednesday said elections on the Indian Ocean islands — where the 500,000 registered electorate also voted for Tanzania's national president — must be carried out again, citing "violations of electoral law".

"The process was not fair and had breaches of the law... I declare all the results to be null and void," Zanzibar Electoral Commission (ZEC) chairman Jecha Salim Jecha said, reporting alleged violations including double-voting and cheating.

On Monday, the main opposition presidential candidate on Zanzibar declared himself the winner before the results were officially announced.

The annulment will likely delay the announcement of full national results. Counting continued for a third day Wednesday, with the ruling party presidential hopeful in the lead.

With 133 of 264 constituencies having released results in East Africa's most populous country, John Magufuli of the long-ruling Chama Cha Mapinduzi (CCM) had won 56.51 per cent of votes.

His nearest rival, Edward Lowassa of the opposition Chadema party, has 41.67 percent, according to official results announced by the National Election Commission (NEC) late Tuesday.

Appeals for calm

But while the CCM is ahead in the presidential race, several key ministers have lost their seats. Those ousted include the ministers for agriculture, information and investment, as well as the mayor of Dar es Salaam, the country's economic hub.

Top NEC official Damian Lubuva earlier dismissed claims of rigging, saying the "baseless and unfounded allegations discredit the commission."

On Zanzibar, police have in recent days fired tear gas to break up crowds, while foreign embassies warned visitors to the popular tourist destination to avoid large crowds.

Security forces on Tuesday surrounded the islands' main tallying and results centre, after opposition challenger Seif Sharif Hamad of the Civic United Front (CUF) repeated warnings that he "will not concede defeat if robbed of my victory."

His main rival is Zanzibar's incumbent president, the CCM's Ali Mohamed Shein.

Troops left the centre later Tuesday, but an AFP reporter in Zanzibar's capital said shots were heard overnight, and that the streets were largely empty on Wednesday, with many shops closed and people saying they were fearful of going out.

Election praised as peaceful

Analysts have warned Tanzania's tight race could spark tensions, with the opposition providing the first credible challenge to the CCM since the introduction of multi-party democracy in 1995.

Many believe 55-year old Magufuli — currently minister of works, for which he earned the nickname "The Bulldozer" — will face a tough challenge from Lowassa, 62.

Lowassa was prime minister from 2005 until his resignation in 2008 over corruption allegations that he denies, and has for years been a CCM loyalist, but on the campaign trail he called for an end to the party's rule.

The ruling party has effectively held power since Tanzania's independence from Britain in 1961, but has suffered a series of defeats at the parliamentary level in this week's election, with eight ministers and other veteran politicians losing their seats.

International observers largely praised the conduct of the vote on Sunday.

"Although there were a few problems in a small number of polling stations, the overall picture was one of millions of people exercising their voting rights in a peaceful environment," European Union election observer chief Judith Sargentini said.

African Union Commission chief Nkosazana Dlamini-Zuma has praised Tanzania for the conduct of the elections, but also warned candidates to put "their country above all other interests" as results are announced.

Outgoing President Jakaya Kikwete, who is not running having served his constitutional two-term limit, has ordered the police to boost security to ensure calm in the country of 52 million people, of whom 22 million were registered to vote.