The allegation against OBP is that it bought FMD vaccines from Biogénesis at R45 (US$2.81) per dose and sold them for between R70 (US$4.37) and R130 (US$8.12) per dose.
BAITS provides authorities with livestock registration and ownership records and supports the management of movements and other animal-health information.
Continued compliance with animal-health measures, including movement controls and disease reporting, will remain necessary to reduce the risk of further spread.
The government expects the work to be completed by the end of August.
The support follows commitments made under the Botswana-Lesotho Binational Commission, where Botswana announced assistance of 100,000 doses of FMD vaccine to Lesotho.
The warning comes as South Africa continues to strengthen its response to foot-and-mouth disease (FMD).