With export hub Ho Chi Minh City continuing to be under social distancing due to surging number of infections, traders and suppliers told Bloomberg that exporters are struggling to transport beans to its ports for shipment.
Shortage of containers and soaring freight rates have worsened the situation.
The Vietnam Coffee-Cocoa Association has urged the government to ease the curbs.
Earlier this week Minister of Transport Nguyen Van The said all types of legal goods must be considered "essential" and their transporters must be allowed to pass through Covid checkpoints.
Authorities in the south need to do everything possible to facilitate the transport of agricultural products such as coffee and rice, he added.
Vietnam is the second biggest coffee producer globally behind Brazil. Last year its exports fell marginally and were worth $2.74 billion.