Jones will be barred from taking charge of their next four matches with the latest a July 4 encounter against Italy in the Nations Championship, while he has also agreed to take a salary reduction.
According to a JRFU statement, the punishment relates to "incidences of verbal abuse" towards match officials during the Japan U23 tour of Australia between April 1 and 15.
He will therefore miss their next few games and will be barred from doing any head coach duties until June 5.
"The Japan Rugby Football Union hereby announces that disciplinary measures will be taken against Eddie Jones, Head Coach of the Japan Men's National Team in accordance with the JRFU's Ethics and Disciplinary Regulations," a JRFU statement read
"These measures relate to incidences of verbal abuse directed at local match officials during the Japan U23 National Team tour of Australia, which took place between April 1 to 15, 2026.
"In addition to the above disciplinary measures, in light of the seriousness of this matter, the JRFU has already decided, based on the contract with him, to impose a salary reduction on him and to suspend him from his duties as Head Coach of the Japan national team for 6 weeks (from April 24 to June 5), and Eddie Jones accepted this decision."
Jones has accepted the sanctions and has apologised to the match officials who were on the receiving end of his comments.
"I accept the disciplinary action of the JRFU relating to the U23 Japan National Team tour of Australia. Some inappropriate remarks that I made caused discomfort to local match officials and other related parties," the Australian said.
"I would like to offer my sincere apologies to everyone involved. I deeply regret my behaviour and words and will make every effort to ensure that this doesn't happen again."
Jones famously took Japan to a historic victory over the Springboks in the 2015 Rugby World Cup but his latest stint in charge, which began after a controversial exit from the Wallabies in 2023, has not been quite as successful.
However, despite this hefty punishment from the JRFU, the former England boss looks set to take the Brave Blossoms into the 2027 World Cup.
Jones was given the vote of confidence by the board at the end of 2025, who feel he is the right man to take them into the global tournament.
"We confirmed that we will continue to support the current structure," said chairman Kensuke Iwabuchi.
"We will support them so that they can move towards the World Cup in a good way."
As such, Jones will miss the following fixtures:
22 May: Japan Select v Hong Kong China Select
29 May: Japan Select v Hong Kong China Select
27 June: JAPAN XV v Maori All Blacks
4 July: Japan v Italy