The Catholic Church in Burundi says it observed "many irregularities" during last week's election that call into question results that delivered victories to the ruling party and its presidential candidate.

The Conference of Catholic Bishops of Burundi said its observers stationed at polling centres across the country witnessed ballot box tampering, officials harassing and intimidating voters, and proxies registered "in place of dead people and refugees".

In an audio statement late Tuesday, the head of the conference, Bishop Joachim Ntahondereye, said the ballot count was conducted in secret, and unauthorised people came and went from the tally room.

"We deplore the many irregularities regarding the freedom and transparency of the electoral process, as well as fairness in the treatment of certain candidates and voters," said the bishop.

"Faced with these, and other irregularities, we wonder if this does not prejudice the (final) results yet to be proclaimed." Burundi's election commission on Monday declared the governing CNDD-FDD party and its presidential nominee, Evariste Ndayishimiye, the winners of the May 20 poll.

No foreign observers

But the final results will not be announced until June 4, when confirmed by the Constitutional Court.

Evariste, a former army general, secured 68.72 percent of the vote while the strongest opposition candidate, Agathon Rwasa, came in a distant second with 24.19 percent.

Outgoing president Pierre Nkurunziza, who has ruled Burundi since 2005 and whose final years were plagued with turmoil, on Tuesday congratulated his successor on a "large victory".

Rwasa and his National Freedom Council (CNL) have already rejected the results and alleged massive fraud, and plan to start filing legal challenges as early as Wednesday.

No foreign observers were allowed into Burundi to keep an eye on the election, which proceeded with scant regard for the coronavirus pandemic.

A church official, who requested anonymity, said the church's push to place monitors in every polling station was rejected but it managed to have close to 3,000 observers across all Burundi's 119 municipalities.

Some of the allegations made by the church mirror those of the CNL, which accused the ruling party of ejecting its officials from polling stations on voting day, and detaining others.

Burundi is tightly controlled by the ruling party and its youth wing has been implicated in a forceful crackdown against the government's critics.

Catholicism is the predominant religion of Burundi's 11 million people. Relations between the church and the government of Nkurunziza, a devout evangelical, soured after the church opposed his third-term bid in 2015.

Violence triggered by Nkurunziza's decision to stay in office left at least 1,200 people dead and pushed 400,000 to leave the country.

In November, the government accused the church of "spitting venomous hatred" after priests delivered sermons denouncing intolerance and political violence ahead of this year's elections.