The number of daily Covid-19 related deaths has matched the previous record from May 8 at 43 deceased.
Japan's Health Ministry also announced 2,432 new coronavirus infections for Friday.
The country’s total nationwide infection stands 158,386 (157,674 on land and 712 on Diamond Princess cruise ship) and death toll to 2,296 (2,283 on land and 13 on cruise ship.)
A further 131,176 patients have been already discharged from the hospitals.
Tokyo reported 449 new cases on Friday, bringing the total number of infections there to 42,793 and 53 patients are in critical condition.
Osaka reported 394 news cases while Hokkaido counted 212.
Prime Minister Yoshihide Suga said in a press conference Friday night that "the new infections and severe cases of the coronavirus infection are hitting record high levels and the situation continues to be extremely alarming. We see the strain on the hospital beds for severe cases and we are dealing with the situation with a full awareness of the crisis."