Japanese media have reported that Jones will be confirmed as head coach of the Brave Blossoms in the coming days after the 63-year-old resigned from the Wallabies role following their disastrous World Cup in France.
Jones had been named Wallabies coach in January on a five-year deal after Dave Rennie was sacked.
Should Jones be confirmed as Japan coach it would be viewed dimly in Australia given that he repeatedly denied reports he had interviewed for the job while preparing the Wallabies for their World Cup opener against Georgia.
Waugh, however, said he did not seen any need to bring up Jones with the Japan Rugby Football Union.
"We’ll play a lot of test matches against Japan and we look forward to continuing that strong partnership," Waugh told reporters.
"I'm not going to buy into speculation around what may have happened or may have occurred.
"We are moving forward to putting all those appointments in place and building a really strong culture for the Wallabies going forward."
Jones coached Japan from 2012-15, engineering a memorable win over South Africa at the 2015 World Cup in England.
Australia hope to name his replacement early next year.
