Jones will miss Japan's Nations Championship opener against Italy in Tokyo on July 4th.
The Japan Rugby Football Union said the 66-year-old Australian violated their ethics and disciplinary regulations during a Japan Under-23 team tour of Australia from April 1st to 15th.
"These measures relate to incidences of verbal abuse directed at local match officials," the JRFU said in a statement.
They said Jones had "accepted this decision".
"I accept the disciplinary action of the JRFU relating to the U23 Japan national team tour of Australia," Jones said in a statement.
"Some inappropriate remarks that I made caused discomfort to local match officials and other related parties.
"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 will not be allowed to take any part in two games pitting a Japan select team against Hong Kong on May 22nd and 29th.
He is also banned from the Japan XV game against the Maori All Blacks on June 27th in Nagoya and the full Japan side's Nations Championship opener against Italy.
He is suspended from duty for six weeks between April 24th and June 5th.