Indonesia's Supreme Court on Thursday overturned the acquittal of two teachers from Canada and Indonesia on charges of sexually abusing kindergarten children at an international school in Jakarta, extended their jail sentences and ordered their re-arrest.

The case, which critics say was fraught with irregularities, has brought the country's justice system under scrutiny and raises doubts about legal certainty in Southeast Asia's biggest economy.

The Canadian embassy in Jakarta called the Supreme Court's decision "unjust" and said the case had not been handled transparently.

"The outcome of this case has serious implications for Indonesia's reputation as a safe place for Canadians to work, travel and invest as well as for Canada's long history of cooperation with Indonesia," it said in an online statement.

Canadian teacher Neil Bantleman and Indonesian teaching assistant Ferdinand Tjiong were convicted on charges of abusing kindergarten students at the Jakarta Intercultural School (JIS), where the children of many expatriates, diplomats, and wealthy Indonesians are enrolled.

The two were originally sentenced to 10 years in jail but were acquitted in August, 2015 after nearly a year behind bars, and released. At least two school janitors remain incarcerated in connection with the case.

"They have been sentenced again, to 11 years," Supreme Court spokesman Suhadi said by phone, referring to Bantleman and Tjiong. The court issued an order for them to be re-arrested.

"It is not clear what evidence the Supreme Court used to overturn the (previous) decision," U.S. ambassador Robert O. Blake said in a statement.

"This continues to raise questions about the veracity of the legal system in Indonesia. This will damage the reputation of Indonesia and how investors view the country," said Keith Loveard of Jakarta-based Concord Consulting.