A leading Egyptian activist who was arrested amid a recent clampdown following anti-government protests has been beaten, threatened and stripped to his underwear while in custody, according to his family.

Mona Seif wrote on Thursday that her brother, Alaa Abdel Fattah, told his lawyers he was blindfolded and threatened that he would never set foot outside Tora, one of Cairo's most notorious prisons.

In a statement, the family reported the details the 37-year-old relayed to his lawyers.

"He was told to strip to his underwear, then forced to talk down a corridor of people as he was beaten on his back and his neck," the statement said.

"This is known as the 'welcome parade' and is routine abuse in Egypt's prisons. It lasted 15 minutes."

The statement added that Abdel Fattah's clothes were stolen, leaving him only in his underwear.

Seif told The Associated Press news agency her brother had filed a legal complaint about the alleged abuses with the State Security prosecutors during a hearing on Wednesday to renew his pre-trial detention.

However, the family said it feared the retaliation of prison authorities.

"By returning to the same prison with the same people who threatened him, we are worried that he might face more violations and more torture," said Seif, a prominent human rights advocate.

She added the family would remain together outside the prison gates until they were allowed to go in to see him and were "assured that he is fine".

Prominent activist

A statement by Marie Arena, the head of the European Parliament Subcommittee on Human Rights, called for Abdel Fattah's immediate release, as well as of his lawyer, Mohamed al-Baqer, who was arrested with him last month.

"I am dismayed that one of the most prominent Egyptian human rights defenders, Alaa Abdel Fattah, is in imminent danger after having been subjected to death threats and torture by state security officers," she said.

Abdel Fattah, who rose to prominence with the 2011 uprisings that swept the Middle East and in Egypt toppled long-time President Hosni Mubarak, was among more than 3,000 people who activists say were arrested since September protests demanding President Abdel Fattah el-Sisi step down.

He was previously released in March, after serving five years in prison for taking part in a peaceful protest.

He was re-arrested last month from a Cairo police station, where he was required to check in every night under the legal terms of his release.

This time, Abdel Fattah is facing several charges, including belonging to a "terrorist organisation" and using social media to spread false news that could threaten national security, his sister said.