It has been almost two years since the Palestinian militant group Hamas led the deadliest attack on Israel in the country’s history.

Not a single person has been charged or prosecuted for it and the entire subject is shrouded in secrecy.

Several hundred Palestinians have been detained on suspicion of direct involvement, and at least 200 of them remain in custody, according to public records. Israeli military officials have said that at least several dozen Palestinians were arrested in or near Israeli territory around the time of the attack on Oct. 7, 2023.

In addition to those detainees, Israel is holding roughly 2,700 other Palestinians who were rounded up in the Gaza Strip over the 21 months since the attack, according to government data. They are suspected of affiliation with Hamas or other militant groups in Gaza, but not necessarily of direct involvement in the Oct. 7 attack.

Israel has killed many of the senior Hamas figures from Gaza who were seen as masterminds of the attack. But some in the country worry that the extensive delays in prosecuting the suspects in custody will allow some perpetrators to escape justice.

Palestinians and rights groups have other concerns.

They say Israel has systematically violated the detainees’ rights by holding them without charge or trial in harsh conditions, with limited access to legal counsel. Sweeping gag orders keep most details of their cases under wraps and for most of these detainees, there is no trace of them in any public records.

The way Israel detains those prisoners “effectively erases these individuals from public awareness and strips them of fundamental rights,” said Nadine Abu Arafeh, a lawyer who has represented detainees from Gaza in other cases in Israeli courts. “Families in Gaza live with questions: Are their loved ones alive?”

Israel’s Justice Ministry declined to comment.

The delays in moving the Oct. 7 cases forward are at least partly because of the chaotic way that law enforcement agents, stretched beyond capacity, collected evidence right after the attack, according to Moran Gez, a former senior prosecutor who oversaw cases of detainees suspected of involvement in the attack, and Yulia Malinovsky, an opposition lawmaker briefed on the issue. The regular criminal justice system was ill-suited to handle the sheer volume of evidence and the compromised state of some of it, they said. Ms. Gez said she retired to open up a private practice.

Israel has extensively documented the atrocities of Oct. 7, in some cases based on footage recorded by the attackers themselves. Several thousand Palestinian militants from Gaza took part in the assault, according to the Israeli military. They stormed more than a dozen communities, a music festival attended by thousands of people, and several military bases in southern Israel.

They killed about 1,200 people and took roughly 250 hostages back to Gaza, in an attack that, according to the United Nations, involved war crimes and possibly crimes against humanity.

Amid upheaval and shock across Israel in the aftermath, investigators skipped many steps in the collection of evidence, according to Ms. Gez and Ms. Malinovsky.

Some bodies were swiftly buried before forensic examination. The volume of killings made it nearly impossible for ballistic experts to trace bullets to specific weapons. Survivors who witnessed the events often did not immediately report their experiences to the legal authorities, and they quickly scattered across the country before the authorities could contact them, said Ms. Gez.

Simcha Rothman, a lawmaker from Israel’s governing coalition, blamed state prosecutors for failing to find ways to adapt legal proceedings to the unusual scale and nature of the attack.

Other considerations may have contributed to the delay in prosecutions.

Israeli security agencies objected to having the cases of attack suspects move forward earlier in the Gaza war, according to Mr. Rothman. But they have since dropped that objection, he said in an interview.

Ms. Malinovsky, the opposition lawmaker, said she believes that senior Israeli officials feared that pursuing the cases could intensify public scrutiny of the failures by the government and military or undermine negotiations to exchange Palestinian detainees for Israeli hostages.

“They don’t want that discourse,” she said of the government.

The prime minister’s office declined to comment on the reasons for the delay in prosecutions. The prison service and Justice Ministry would not provide any information on the detainees.

Lawmakers in Israel recently took a first step toward putting some of those suspected of direct involvement on trial. The Knesset, or parliament, passed an initial vote in late May to establish a dedicated tribunal to try suspects in the attack.

But the bill requires several more votes, and it will likely be months before the first detainees go to court.

Mr. Rothman and Ms. Malinovsky were co-authors of the bill, which was meant to bypass legal hurdles to prosecutions by establishing a special tribunal of 15 judges with some capacity to override the ordinary criminal system. The bill proposes charging participants in the attack with offenses of genocide, which are punishable by death under Israeli law.

Other countries have created similar tribunals in response to war or mass atrocities, said Yuval Shany, a senior researcher with the Israel Democracy Institute, a Jerusalem-based research group. For example, U.S. military commissions were set up to prosecute Al Qaeda suspects after the Sept. 11, 2001 attacks on the United States, he said.

Mr. Shany said international law experts are generally critical of such special courts as they often lead to an erosion of legal standards.

All of the roughly 2,700 Palestinians detainees who were rounded up in Gaza over the course of the war are designated as “unlawful combatants,” which, according to Israel law, means they can be held without charge or trial.

Under the terms of a cease-fire earlier this year, Israel released about 1,000 of the “unlawful combatants” to Gaza, in addition to women and minors detained in Gaza over the course of the war.

If negotiations between Israel and Hamas over a new cease-fire progress to a deal, some of the remaining detainees could potentially be exchanged for the remaining hostages in Gaza.

The lengthy detention of so many people without trial “risks becoming a life sentence without the usual protections of the criminal process,” said Monica Hakimi, a Columbia Law School professor and an expert on international law.

At least 48 of these Palestinian detainees have died in custody, according to data from the military and prison service provided in response to freedom of information requests filed by Physicians for Human Rights — Israel, a rights group.

Former detainees told The New York Times last year that they were punched, kicked and beaten with batons, rifle butts and a hand-held metal detector while in custody. Two said their bones were broken and three said they had received electric shocks during their interrogations.

The Israeli military denied that “systemic abuse” had happened in a base where thousands of Gazan detainees had been held earlier in the war. The Shin Bet, Israel’s domestic intelligence agency, said that all of its interrogations were “conducted in accordance with the law.”

In February, the Israeli military charged at least five soldiers who served in that base with abuse of a detainee.

Itamar Ben-Gvir, Israel’s minister of national security who oversees the country’s prison service, posted two videos in January of a facility where some Gazan detainees suspected of involvement in the Oct. 7 were held. The videos showed a subterranean prison ward in Ramla, a town in central Israel.

“I won’t forget the murders and horrors,” Mr. Ben-Gvir said in one of the videos, suggesting that the prisoners were connected to the attack. He then pointed at three handcuffed men kneeling in brown uniforms, their heads bowed. “Look at them now, how cowardly they are.”

In late July, Israeli lawmakers extended emergency provisions that allow the ongoing detentions of prisoners suspected of involvement in the attack in detention awaiting prosecution through January 2026 — an indication that they may not face charges for at least six more months.

“This is a problem,” Mr. Rothman told lawmakers before the extensions.. “It’s a malfunction.”

Patrick Kingsley,Aaron Boxerman and Natan Odenheimer contributed reporting.