Riots have erupted in Burundi's capital over the president's decision to stand for a third electoral term, raising fears that violence could become ethnicised.

On April 25 Burundi's leading political party, CNDD-FDD endorsed current president Pierre Nkurunziza as their candidate in the national election on 26 June. This meant Nkurunziza would be standing for a third term, despite the constitution only allowing a president to be elected for two terms.

Opposition supporters took to the streets of the capital Bujumbura to demonstrate against a decision that was seen as being unconstitutional. Reports suggest that at least 12 people have been killed in the protests, although the police say the figure is lower, but the disturbance continued throughout the week. The United Nations said today that nearly 40,000 refugees have fled into neighbouring Rwanda, Tanzania and the Democratic Republic of Congo in the last month.

Nkurunziza argues that his first five-year term doesn't count as, owing to the transitional process at the end of the civil war, he was chosen by parliament and not the people of Burundi. Yesterday the constitutional court ruled in his favour, although there are widespread reports that members of the court were pressured into agreeing with the President. The court's vice-president fled to Rwanda because he refused to sign the ruling.

The foreign and commonwealth office said in a statement today: "Reports of intimidation against members of the Constitutional Court do not give the impression of an independent court that was able to come to an impartial decision. This is not in the best interests of Burundi or its people."

US Secretary of State John Kerry called on Nkurunziza to abandon his election plans. On Monday he told reporters: "We are deeply concerned about President Pierre Nkurunziza's decision, which flies directly in the face of the constitution of this country."

The Burundian government has described the protests as "insurrection". Police arrested leading human rights activist Pierre Claver Mbonimpa and Human Rights Watch said on Friday that more than 400 people had been detained.

It is the worst uprising in the country since the end of the 13-year civil war in 2005, in which an estimated 300,000 people died. Since independence in 1962 there have been ongoing tensions between the Hutu and Tutsi populations, leading to fierce violence between the two ethnic groups in 1972 and again in the 1990s.

There are fears that the protests could spread and that they could become ethnicised. But Simon Guillebaud, the founder of Great Lakes Outreach who has lived in Burundi for 16 years, told Christian Today that Burundi has "moved on" from ethnic conflict, although he said there are "a few people who are trying to make it an ethnic issue."

Speaking of the situation before the protests, he said the Arusha peace agreement, signed in 2000, and the subsequent constitution had been effective in making Tutsis feel safe. He added that the political parties were not divided along tribal lines.

"What we've experienced has been less than Baltimore," Guillebaud said, criticising John Kerry's remarks for being "out of order". He said that the international press had been "more alarmist than the realities on the ground."

Even so, Guillebaud wrote on his blog last week: "There is great fear in the air. It's impossible to predict how things will pan out, and whether this might be quickly resolved or drag on for ages and even spill over into other nations. Optimists are few and far between, and the stakes are incredibly high for the nation and beyond."

In a message to supporters on Saturday he said that demonstrators had set up barricades on their street but they had not been targeted but had spoken with the protestors. He added: "We'd obviously prefer constant calm, but sometimes a storm comes along. Whether for us that's this Monday or not, God has done so many amazing things in Burundi over the years. Some of his finest troops are Burundian. So let's continue to be in faith, not in fear, recognising the realities but pleading with and trusting God for breakthroughs and solutions that through our own eyes are hard to discern as things stand."

The World Council of Churches and the All Africa Conference of Churches issued a joint statement calling for peaceful dialogue and prayer for the nation. "The current atmosphere of division places in jeopardy the peace agreement which has aimed at bringing an end to conflict," they said in the statement. "While reasonable people may differ on the specifics of the road ahead, it is essential that violence cease and dialogue be re-established, so that justice may prevail.

"Beyond the issues at play in the current confrontation, it is not only the peace and security of Burundians which are at stake but also the stability of the Great Lakes region."