Rabbi Abraham Cooper, an associate dean at the centre whose primary focus in the past has been Holocaust education, told Associated Press the move was unprecedented.
Mitsubishi Materials Corp senior executive Hikaru Kimura expressed remorse that prisoners had been put to work in mines operated by the firm.
Murphy, 94, said: "I listened very carefully to Mr Kimura's statement of apology and found it very very sincere, humble and revealing.
"We hope that we can go ahead now and have a better understanding, a better friendship and closer ties with our ally, Japan."
The mines operated at four locations run by Mitsubishi's predecessor company, Mitsubishi Mining Co.
Mitsubishi's apology came independently of the Japanese government, which apologised in 2009.
At least 650 British soldiers were also forced to work in the camps and the apology has prompted calls for Mitsubishi to extend it to the UK.
The Java FEPOW Club, which represents British prisoners of war veterans in the Far East, told PRWeek it was upset at the terms of Mitsubishi's apology and called on other companies that were complicit in forced labour to apologise as well.
A spokeswoman said: "The fact that this is pointed at American prisoners of war only is a little upsetting because thousands of British, Australian, Dutch - and hundreds of thousands of Asians - were also held prisoner, and made to work in abhorrent conditions with unbelievable treatment for three-and-a-half years. It is good that Mitsubishi is recognising its part in this, but it must remember all nationalities."
Meanwhuile, Vera Houghton, widow of RAF prisoner Leslie Houghton, told a newspaper that an apology was overdue.
She said: "Even if they had done it in 1950, people would have accepted it. But this apology is not coming from the people who did these things. It is coming from their grandchildren."
Mitsubishi in the UK was contacted but did not respond to requests for comment.