Doctor Adnan Ahmed Atiya al-Barsh died at the Israeli-run Ofer prison in the occupied West Bank last month, the Palestinian Prisoners Affairs Committee and the Palestinian Prisoners Club said in a joint statement.
Contacted by AFP about the reported death in custody, the Israeli army said: "We are currently not aware of such (an) incident."
Barsh, 50, had been arrested with a group of other doctors last December at Al-Awda Hospital near the Jabalia refugee camp in northern Gaza.
He died on April 19, the prisoners groups said, citing Palestinian authorities.
"His body is still being held," they added.
The groups said they had also learnt that another prisoner from Gaza, Ismail Abdel Bari Rajab Khadir, 33, had died in Israeli custody.
Khadir's body was returned to Gaza on Thursday, as part of a routine repatriation of detainees by the army through the Kerem Shalom border crossing, the groups said, citing authorities on the Palestinian side of the crossing.
The groups said evidence suggested the two men had died "as a result of torture".
They alleged that Barsh's death was "part of a systematic targeting of doctors and the health system in Gaza".
The health ministry in Hamas-ruled Gaza said the surgeon's death amounted to "murder", adding that it brought to 492 the number of health workers killed in Gaza since the war erupted nearly seven months ago.
The prisoners groups said the latest deaths brought to 18 the number of deaths in Israeli custody since the war began on October 7.
There have been repeated Israeli military operations around Gaza's hospitals that have caused heavy damage.
Medical facilities are protected under international humanitarian law but the Israeli military has accused Hamas of using Gaza's hospitals as cover for military operations, something the militant group denies.
The Al-Shifa hospital, where Barsh worked, has been reduced to rubble by repeated Israeli military operations, leaving what the World Health Organization described last month as an "empty shell".
The war started with an unprecedented Hamas attack on southern Israel that resulted in the deaths of 1,170 people, mostly civilians, according to an AFP tally of Israeli official figures.
Israel estimates that 129 captives seized by militants during their attack remain in Gaza. The military says 34 of them are dead.
Israel's retaliatory offensive against Hamas, has killed at least 34,596 people in Gaza, most of them women and children, according to the health ministry.
