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).