Hunger-strikers being force fed at Guantánamo Bay are shackled to a chair, fitted with a mask and have tubes inserted through their nose and into their stomachs for up to two hours at a time, according to revised guidelines in use at the camp.

The guidelines, which were updated after the latest protest by inmates began in February, detail the process of involuntary feeding and how after the sessions, detainees are kept in a "dry cell" to prevent them vomiting. News of the 30-page Standard Operating Procedure (SOP) manual – which was first published on Monday, by al-Jazeera, and has since been confirmed to be genuine by the US military – comes amid fresh questions over the ethics of force-feeding protesters at the prison.

It comes as consortium of human rights activists, pressure groups and law bodies issued a direct plea to US defense secretary Chuck Hagel to end the practice of force feeding at Guantanamo Bay.

Signed by 20 organisations including the American Civil Liberties Union, Human Rights Watch, the Center for Constitutional Rights and NYU School of Law's Global Justice Clinic, the letter to Hagel says the force-feeding of competent prisoners constitutes "cruel, inhuman and degrading treatment".

The letter notes that leading international medical bodies have come out against the force-feeding of detainees. Moreover, as practised at Guantánamo Bay, it violates the Geneva conventions, the signatories claim. There has been growing disquiet over force-feeding at the camp in recent weeks, from both human rights activists and the medical community.

An editorial published earlier this month in the medical journal the Lancet suggests that there is a distinct moral line between force-feeding people who are refusing meals through impaired mental capacity and those doing so as a protest. It states: "In the latter case, the individual has weighed up the facts, and come to the conclusion that they will refuse nutrition, and risk death in order to correct a perceived injustice. Whether or not one agrees with this decision, to force-feed infringes the principle of patient autonomy."

The Lancet editorial concludes that it "can only be hoped that those health workers responsible for the care of detainees act in an ethical manner: both for the benefit of the individuals concerned, and for the standards of humanity and dignity that both the medical profession, and the USA, are pledged to uphold".

The new guidelines for medical management of hunger strikers at Guantánamo Bay were implemented two months ago. By Monday, 100 of the 166 detainees at the camp were refusing food. Of those, 29 were being force-fed, with five in hospital.

According the revised SOP, which was introduced on 5 March – one month into the current protest – those subjected to forced feeds are shackled to a chair. A "mask is placed over the detainee's mouth to prevent spitting and biting". A tube is then inserted through a nostril and fed through the nasal passage to the stomach. Once the tube is taped into place, feeding begins. The SOP suggests that force-feeding can be completed in 20 to 30 minutes but that it can last up to two hours. On completion, inmates are placed in a "dry cell" without running water and watched for up to 60 minutes, for any "indications of vomiting or attempts to induce vomiting".

Those who have been subjected to the procedure have spoken about the pain and degradation they feel during it. In an op-ed for the New York Times last month, Samir Naji al Hasan Moqbel wrote: "I will never forget the first time they passed the feeding tube up my nose. I can't describe how painful it is to be force-fed this way. As it was thrust in, it made me feel like throwing up. I wanted to vomit, but I couldn't. There was agony in my chest, throat and stomach. I had never experienced such pain before. I would not wish this cruel punishment upon anyone."

Moqbel's legal representative, Clive Stafford Smith, attempted to speak to the inmate last Friday. But Moqbel, along with another inmate, declined the telephone call. It has been suggested that guards are now subjecting inmates to humiliating body searches if they want to speak to lawyers. Another lawyer, David Remes, told AFP over the weekend that two men he represents had declined calls. "Under the new search policy, a detainee who leaves his camp is subject to a search including his private parts and holding his private parts," Remes alleged.

According to AFP, he added that the "shocking" searches were "designed to deter many detainees from meeting with their clients … to make their life more miserable and put the detainees in front of an impossible choice".

Stafford Smith tweeted that two clients of his legal charity Reprieve had "refuse[d] legal calls. Referring to the remarks made by Remes, he added that "new military policy is to sexually abuse them in searches".

Authorities denied that the searches were anything more than a "pat-down". A US military spokesman, Lt Col Samuel House, told the Guardian: "Full frisk searches are conducted in a professional manner to quickly locate and identify contraband hidden on the body. The searches are conducted with clothes on, similar to a pat-down search conducted by an airport security screener."

If a detainee refuses to be searched when leaving his cell for routine visits, such as a non-emergency medical appointment or a legal call, guards are obliged not to take them. House added that this policy was introduced "in light of contraband discovered during recent cell searches".