The Association for Human Rights Legal Aid (AHRLA) said the body of 31-year-old Muhammad al-Sayyed was retrieved from a hospital a week after he and his younger brother were arrested on 14 September.
Sayyed's body was covered in "bruises, his skull was fractured and his nails pulled out", the association said on Tuesday.
However, his brother was released unharmed.
In a separate incident, AHRLA said Ahmad Muhammad Omar was locked in a cold-storage room for 23 days by a police officer, and he was later injected with "contaminated substances".
The group said he later died in hospital from gangrene.
Egyptian officials could not immediately confirm the deaths, but under Egyptian law, people found guilty of torture face up to 15 years in prison.
Associations in Egypt and international rights groups regularly denounce cases of torture and mistreatment in Egypt's prisons and police stations.
In human rights report on Egypt last year Amnesty International blasted the Egyptian government.
Thousands of suspected supporters of banned Islamist groups remained in detention without charge or trial, Amnesty said.
Others were serving sentences imposed after grossly unfair trials before military courts.
And torture and ill-treatment of detainees continued to be systematic.