Some 600 pygmies, or Twa, have fled Burundi for neighbouring Rwanda to escape persecution and hunger, officials say.
Twa MP Liberata Nichayenzi said the majority had fled because of intimidation by ethnic Hutus.
The Hutus accuse the minority Twa of voting against the new power-sharing constitution last week.
Correspondents say the Twa are often accused by Hutus of being allied to ethnic Tutsis.
They have mostly fled the drought-hit north-eastern Kirundo province.
Ms Nichayenzi said a Burundian delegation would travel to Rwanda soon to persuade the Twa to return home.
The Twa account for some 1% of Burundi's population; Tutsis are 14% and Hutus 85%.
The constitution was passed with an overwhelming majority.
By establishing a formula for Hutus and Tutsis to share power, the constitution is intended to end 12 years of bloody ethnic conflict.
Some Twa leaders have accused both major groups of marginalising them.