The defence ministry said in September it would not accept new recruits into a programme that trains Myanmar military personnel.
But Andrews criticised the decision to allow soldiers already in the programme to complete their training.
“They are receiving combat training and learning how to be effective soldiers and commanders” and will return “to a military responsible for crimes against humanity and war crimes”, he said.
“So long as the defence ministry continues to train Myanmar soldiers, Japan’s Self-Defense Forces will be linked to a brutal military regime.”
Japan has longstanding ties with Myanmar and was a major provider of aid, as well as a source of investment, before the coup.
Andrews said he had urged Japan to redirect money that would have gone into new aid programmes toward funding food rations for Rohingya refugees in neighbouring Bangladesh.
Around a million Rohingya are in the country, most of them arriving after a 2017 military crackdown by Myanmar that is now subject to a UN genocide investigation.
Food rations were already cut by 17 per cent last month, but now face being reduced an additional 20 per cent, Andrews said, risking “irreparable harm to Rohingya children”.
Some Japanese businesses, including drinks giant Kirin, have exited Myanmar, but Andrews said others continue to cooperate with partners that serve the junta or have sold operations to junta-linked firms.
The former US congressman and Myanmar campaigner said the international community as a whole was “failing the people of Myanmar”.
“The fact is, conditions are deteriorating quickly and it means that we need to reassess our actions.”