Three female lions died at Tama Zoological Park in Hino, in the Tokyo metropolitan area, over six days from 28 July to 2 August.
The park identified the animals as Mugi, aged three, which died on 28 July; Ichigo, aged 11, which died on 31 July; and Luena, aged 15, which died on 2 August.
Health problems among lions at the enclosure included fatigue, reduced appetite and difficulty standing.
Staff used fans, water cooling measures, intravenous fluids, medication and vitamins in an effort to treat affected animals.
The park found dehydration and signs of organ failure in the three dead lions, findings that it and cited specialists linked to heat stress; a final post-mortem report was still pending.
The park temporarily closed its lion exhibit as animals became ill.
Four lions were reported to be improving, while three remained under treatment.
The park said the healthy and recovering lions would be kept in areas equipped with portable air conditioners and large industrial fans.
Parts of Japan experienced temperatures above 40 degrees Celsius during the heatwave.
Veterinary professor Hideaki Karaki said lions cannot cool themselves by sweating and that high humidity can limit the effectiveness of their rapid breathing in lowering body temperature.