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The vote was the last in a series which has already seen separate assemblies and presidents elected on each of the three islands, in a bid to end decades of strife between the federal and regional powers.
More than half of eligible voters in the coup-prone nation of 630,000 people participated, according to an estimate given by national election commission head Mohamed Rachade.
In the first result announced hours after the poll, the federal defence minister Hamada Madi Bolero, who is closely linked to federal President Azali Assoumani, lost his race.
Bolero was beaten by Elarif Oukache, a member of the autonomous regional government on Moheli, the smallest of the three islands, said a local official of the national election commission.
Other preliminary results were expected later in the evening.
Despite persistent political tensions and one candidate's direct verbal attack on international election monitors, Sunday's election went smoothly but ended earlier than the planned 6:00 pm (1500 GMT) closure.
"Everything is going fine, apparently... aside from a few incidents which didn't get out of hand", said Abraham Zinzindohoue of Benin, the chairman of the international commission that is to validate the results.
Zinzindohoue said the polling stations had shut early "simply because everyone had already voted".
Friday saw trouble between the island rulers and Zinzindohoue's commission, while on Sunday Mohamed Chafiou, a candidate on the main island, urged his supporters not to vote, saying it was pointless.
In last week's first round, Chafiou initially won a lead of 52 percent in his constituency on Grande Comore, slightly ahead of Mohamed Chatur, an Azali backer.
However, the independent commission validating the results annulled the vote in that district on the grounds of fraud.
"For me, this election is pointless," Chafiou told AFP. "The first round made me the winner. There was no motive for annulling it."
His opponent, Chatur, commented that he "would have liked competition, but that's the way it goes".
Sunday's poll culminates a process of devolution to bring stability to one of the poorest and most coup-prone countries in the world. It began with a new 2001 constitution, which gave each island considerable autonomy.
The former French colony, which lies between Africa's southeastern coast and the vast island nation of Madagascar, has been rocked by 20 coups or coup attempts in the past quarter century.
Some 225,000 voters were electing 18 of the 33 deputies who will sit in the federal assembly on the main island, Grande Comore. The other 15 members will be appointed by the separate parliaments of each island.
Sunday's vote came in the wake of an outburst of hostility by the presidents of the three islands to the international commission.
On Friday they demanded that Zinzindohoue, the Beninese lawyer who heads the commission, be replaced, and pulled their own representatives out of the body.
Zinzindohoue was blamed for what the island leaders jointly described as "repeated interference at all levels of the electoral process".
Benin's former supreme court president dismissed the allegations, saying the "commission comprises judges of integrity who work in collegiate fashion", and he won a statement of support from the international community.
In the first round of the vote last Sunday, the island delegates took the lead over those of federal president Azali.
The latest national crisis began more than three decades after independence in 1975. Anjouan and Moheli unilaterally seceded in 1997, before returning to the fold under new constitutional arrangements.
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