Canadian teacher Neil Bantleman (L) and Ferdinand Tjiong inside a holding cell. (Reuters)

Indonesia has granted clemency to a Canadian teacher convicted of sexually abusing students, an official said on Friday, in a case that critics say was riddled with irregularities and threw a spotlight on the Southeast Asian country's justice system.

Neil Bantleman and Indonesian teaching assistant Ferdinand Tjiong were convicted in 2014 on charges of abusing kindergarten students at the Jakarta Intercultural School, where the children of many expatriates, diplomats and wealthy Indonesians are enrolled.

The pair have always maintained their innocence and the lack of transparency in the case was criticised by Canada and the United States, adding to concerns about the lack of legal certainty in Southeast Asia's biggest economy.

Sri Utami, director general of correctional affairs at Indonesia's Law and Human Rights ministry, confirmed in a text message to Reuters that Bantleman had been granted clemency.

Bantleman's brother Guy said in a statement: "I am pleased to confirm that my brother Neil has safely returned to Canada."

Bantleman was cited in the statement as saying: "Five years ago I was wrongfully accused and convicted of crimes I did not commit and furthermore never occurred."

Canadian media said teaching assistant Tjiong remained in jail.

The two were originally sentenced to 10 years in jail but were acquitted in August 2015, after nearly a year behind bars, and released.

However, Indonesia's Supreme Court later overturned the acquittal, extended their jail sentence and ordered their re-arrest, a decision the Canadian embassy in Jakarta called unjust.

Bantleman in his statement thanked family and friends around the world for their support and "the Government of Canada for their steadfast commitment to seeing us home".

"We are asking for privacy at this time so we can reconnect with family and move forward with our lives," he said.