Belgium had summoned the Burundian ambassador in Brussels on Friday to explain reports that the accreditation of the envoy, Marc Gedopt, had been withdrawn.
Burundi has asked its former colonial power Belgium to replace its ambassador because it has lost confidence in him, a senior official said on Monday.
Salvator Ntacobamaze, permanent secretary in Burundi's Ministry of External Relations and International Cooperation, gave no further explanation for the action.
A Belgian Foreign Ministry spokesman said Belgium viewed the request as an "unfriendly act" but had yet to decide on a course of action and would keep channels of communication open with Burundi's government.
Bilateral relations have deteriorated since Belgium said this month it would halt some aid in protest at Pierre Nkurunziza securing a third term as president of the central African country.
"Through a verbal note, the government of Burundi asked its counterpart for the replacement of the Belgian ambassador to Burundi since it has no more confidence in him," Ntacobamaze told Reuters.
Belgium had summoned the Burundian ambassador in Brussels on Friday to explain reports that the accreditation of the envoy, Marc Gedopt, had been withdrawn. Gedopt is not in Burundi at present.
Belgian aid for Burundi was just under 50 million euros ($56 million) in 2013, most of it going directly to the state.
Burundi has experienced turmoil and sporadic violence since April, when Nkurunziza announced he was seeking a third term, a move the opposition says violated the constitution and a peace deal that ended civil war in 2005.
He was sworn in on Aug. 20 after winning an election boycotted by his opponents.