The 100 Australian containers are part of a total of 547 containers that Indonesia has inspected and found to be polluted by so-called B3 waste.
Indoneisan Director-General of Customs Heru Pambugi said three companies "had been found to have imported plastic waste mixed with rubbish and B3 waste".
One of the companies did not have the required documents, he said.
Those companies were responsible for importing all 100 of the Australian containers being returned.
Customs, Heru said, was acting on the instructions of President Joko Widodo and the decision to return the containers showed the consistency of the government of Indonesia on the importation of plastic waste.
Earlier, Indonesia had planned to return a number of containers containing plastic waste to different countries, including the US, Spain, the UK, Germany, France, Greece, the Netherlands, Slovenia, New Zealand and China.
For Australia, in July this year, local media reported that Indonesia also sent back eight containers of trash seized in Surabaya and one in Batam. One month later, the Australian Government announced that the country will not export plastic waste, paper and crystal to other countries where they could be released to the ocean.