The figures, which included overseas fee-paying students in primary, secondary and tertiary education in the January to April 30 period this year, also showed New Zealand numbers, at 56,238, dropped 6% compared with the corresponding time last year.
Education Dunedin chairman Stephen Higgs said it was a little pleasing numbers had declined at a slower rate in Otago, but noted the high New Zealand dollar had made it ''tougher'' for institutions across the country.
International students remained important for both the Dunedin and Otago economies, Mr Higgs said.
''It's hugely important. There has been some work done previously that would indicate the overall economic impact of those students is $200 million for the Dunedin economy.''
The ministry figures also showed Otago was the fifth most popular destination for international students after Auckland (34,222), Canterbury (4472), Waikato (3676) and Wellington (3617).
In the past decade, overseas numbers peaked in 2004, both nationally and in Otago, with 72,013 and 3586 overseas students respectively.
The most drastic change could be seen in Canterbury, which had a 65% drop in overseas students since 2004 when there were 12,638 in the province. The drop was most evident after the Christchurch earthquakes.
The ministry data was used as part of Education New Zealand's International Education Snapshot report for January 1 to April 30, released last week.
The figures included were slightly different from the ministry figures, in part due to PhD students being included. It showed a 3% decline in international student numbers in New Zealand.
Tertiary Education Minister Steven Joyce put a positive spin on the decline, saying the sector was performing well.
''While overall enrolment numbers are down slightly, our international education sector is continuing to perform well, with the [Tertiary Education Commission] reporting a further $25 million increase in international fees at tertiary institutions to $404 million in the year to June,'' Mr Joyce said.
