Burundi's powerful ruling party chairman took refuge briefly in the South African embassy on Monday night.
Ex-President Ndayizeye (l) was acquitted of plotting a coup
Hussein Radjabu said he had been alarmed by a sudden switch of his bodyguards, but has since received reassurances about his safety.
There have been calls for him to be sacked after the acquittal of a former president accused of plotting a coup.
Government ministers have warned the ruling party split could endanger the peace process that ended the civil war.
Burundi, one of the world's poorest nations, is emerging from a 12-year conflict.
Critics say the coup plot implicating ex-President Domitien Ndayizeye was invented by leading ruling party figures, including Mr Radjabu, to quell dissent.
Mr Ndayizeye and four others were acquitted on charges of plotting to assassinate the president.
Six government ministers have called on the president to resolve the political crisis engulfing the mainly Hutu FDD party, AFP news agency reports.
The ministers had "deep concerns at the attempts at internal division which have shaken our party and which are in danger of affecting the peace", Trade Minister Jean Bigirima said.
Mr Ndayizeye - a transitional president - was succeeded by Pierre Nkurunziza, a former rebel leader who was elected by a landslide in 2005.
Since independence in 1961, Burundi has been plagued by tension between the dominant Tutsi minority and the Hutu majority.
More than 300,000 people have died in the war sparked in 1993 by the assassination of Burundi's first Hutu head of state and democratically-elected president, Melchior Ndadaye.