An additional 237 staff members will be deployed at selected ports.
"All departments and agencies have provided for officials at ports to work overtime in order to deal with the expected increase in traveller movement and to avoid congestion," the department said.
The Lebombo border post between South Africa and Mozambique will operate all day and night from April 17 to April 29.
The Oshoek border post between South Africa and Swaziland will also operate around the clock from April 18 to April 21.
Other busy border posts will have extended operating hours - from between one and six hours.
Beitbridge, Maseru and Ficksburg border posts will continue running 24 hours a day as usual.