Two years after Islamist president Mohamed Morsi's ouster, Egyptian authorities have continued their onslaught on young activists to crush dissent, in a sign that the country has regressed into "all-out repression", Amnesty International said on Tuesday, in a report Egypt's government has qualified as "false allegations" and "lies".

In the report released on Tuesday, the London-based rights watchdog criticised what it called a "blatant attempt" by the Egyptian authorities to "nip in the bud any future threat to their rule".

Amnesty looked at the cases of 14 young people among thousands it said were arbitrarily arrested, detained and jailed in Egypt over the past two years in connection with protests.

"Mass protests have been replaced by mass arrests," the group said on the second anniversary of the 30 June massive protests that toppled Islamist president Morsi after a sole year of divisive rule.

"By relentlessly targeting Egypt’s youth activists, the authorities are crushing an entire generation’s hopes for a brighter future,” said Hassiba Hadj Sahraoui, deputy director of the Middle East and North Africa Programme at Amnesty International.

Following the 2011 uprising that toppled long-time strongman Hosni Mubarak, youths were seen as the catalyst of change in a country long oppressed under autocrats.

"Yet, today, many of these young activists are languishing behind bars, providing every indication that Egypt has regressed into a state of all-out repression," said Sahraoui.

Amnesty said a crackdown led by President Abdel Fattah El-Sisi has seen more than 41,000 people arrested, charged or indicted with a criminal offence, or sentenced after unfair trials.

“The scale of the crackdown is overwhelming," Sahraoui said. "The Egyptian authorities have shown that they will stop at nothing in their attempts to crush all challenges to their authority.”

Foreign ministry spokesman Badr Abdelatty denied that Egypt is targeting youth activists, saying in a statement on Tuesday that Amnesty had presented "false allegations" and "lies" in its report.

Egyptian officials accuse rights organisations of serving foreign agendas that aim to undermine the country's security and stability, a view the spokesman reaffirmed on Tuesday.

The rights group said that the clampdown initially began with the arrests of Morsi and his supporters, but has rapidly expanded to include the country's entire political spectrum.

It said a new round of arrests in mid-2015 saw at least 160 people detained "in conditions amounting to enforced disappearance".

Amnesty claimed that not a single member of the security forces has faced criminal charges over the deaths of hundreds of Morsi supporters at Cairo protest camps on 14 August 2013.

Foreign ministry spokesman Abdelatty said that the organisation "lacks credibility" by addressing developments in Egypt from "a biased, subjective perspective that raises questions".

He slammed what he called Amnesty's "politicised policy" of relying on "unknown and undocumented sources" for its information, while ignoring official censuses and reports.

Amnesty urged Egypt's western and European allies not to "sacrifice" human rights in their talks with the authorities, saying there had been "no indication that stopping gross human rights violations in Egypt was on the agenda" during previous meetings.

"The gross hypocrisy of Egypt's partners has been laid bare in a race for lucrative business deals, political influence and intelligence, as well as new sales and transfers of policing equipment that could facilitate human rights violations," Hadj Sahraoui said.

On Monday, the group condemned as "despicable, cowardly and cold-blooded" the killing of late prosecutor-general Hisham Barakat, whose convoy was struck by a car bomb in Cairo earlier on the same day.

"If the rule of law is to prevail in Egypt, judges and prosecutors must be free to do their job without the threat of violence," Amnesty said, urging authorities not to respond with further repression.