Nyambene Miraa Trade Association (Nyamita) protested that the portal provided to exporters by AFA only allowed companies registered in Djibouti.
Agriculture and Food Authority Director General Bruno Linyiru said the authority was working with the Kenyan Embassy in Djibouti to resolve the challenges.
Miraa farmers will have to wait longer to benefit from the multimillion-shilling market in Djibouti after prospective exporters encountered challenges registering for certification.
Two weeks ago, the Agriculture and Food Authority (AFA) announced that Kenya had secured a miraa market in Djibouti, with the potential to take in 20 tonnes daily. This could earn farmers more than Sh20 million daily, based on minimum prices set by Agriculture Cabinet Secretary Mutahi Kagwe earlier this year.