The success rate for Sri Lankan applicants was 21 percent, down from 50 percent.
The decline in the percentage of visa approvals started to become prominent from October last year, the association said.
The agency also said Wednesday 412 foreigners living in Japan were stripped of their student status in 2018, more than double the 172 who lost their student visas the year before, for failing to follow requirements.
The tightening of regulations on student visas signals Tokyo's push to shift to a new visa program introduced this April to bring in more mainly blue-collar foreign workers to the country's labor-hungry sectors.
Foreigners on student visas can only legally work up to 28 hours a week, but those with the new visa status of skilled worker can work as much as their Japanese counterparts.