Officers and troops were ordered to stay off the links after Monday's declared test.
"The virtual ban on golfing is effective at all military golf courses across the country," a defense ministry spokesman said.
Some courses had already decided to refuse to take reservations as the whole military has been ordered to maintain an alert.
Defense Minister Yoon Kwang-Ung sent an e-mail to his troops, reiterating his call for military preparedness against North Korea.
"We ... should maintain perfect military readiness 24 hours a day to instantly cope with North Korea's threat and provocation," the message said.
There are dozens of subsided military golf courses throughout South Korea and the past time is a popular one with troops.
The republic does still treat golf with some suspicion as it continues to carry the stigma of being associated with wealth, the neglect of duty and corrupt business links.
In March Prime Minister Lee Hae-Chan and Vice Education Minister Lee Gi-Woo stepped down after a golf outing with businessmen sparked a criminal investigation into alleged influence-peddling.
South Koreans were also upset that the ministers were out on the greens instead of addressing a railway strike that briefly crippled the country.
The sport is also popular in North Korea -- where, according to the communist state's official media, leader Kim Jong-Il scored 11 holes-in-one in his first attempt at golf, a feat that would make him the greatest golfing prodigy of all time.