Judge Sylvere Nimpagaritse told AFP that the court's judges had come under "enormous pressure and even death threats" from senior figures, which he refused to name, to rubberstamp the controversial candidature of the president.
His dramatic departure yesterday comes after more than a week of protests in the central African country in which at least 13 people have died, including four protesters shot dead by police yesterday.
Nimpagaritse claimed that a majority of the court's seven judges believed it would be unconstitutional for Nkurunziza to stand again.
"In my soul and conscience I decided not to put my signature to a ruling, a decision which is clearly not lawful that would be imposed from the outside, and which has nothing legal about it," Nimpagaritse told AFP before leaving the country.
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Nkurunziza, a former rebel leader and born-again Christian from the Hutu majority, has come under intense international pressure to withdraw from the June 26 presidential poll.
Burundi, where a 13-year civil war ended only in 2006, has been rocked by violent protests since the CNDD-FDD designated Nkurunziza to stand in apparent defiance of the constitution and the Arusha accords which ended the war.
His supporters say he is eligible to run since his first term in office followed his election by parliament - not directly by the people as the constitution specifies.
The country's powerful security forces appear divided over Nkurunziza's bid to hold onto power, diplomatic sources told AFP.
rules of Burundi and of those who govern it".
But a statement by Defence Minister General Pontien Gaciyubwenge on Saturday appeared to contradict this, declaring
the army's neutrality and calling for an end to attacks on citizens' rights.