The authorities blame Taliban insurgents notorious for their opposition to schooling for girls, saying the hardline Islamists have poisoned water supplies or somehow gassed the pupils -- winning headlines around the world.
But the human rights unit of the UN mission in Afghanistan (UNAMA) has raised concerns that the confessions might be suspect.
"The UN is unaware of any forensic evidence to support the allegations that poison has been used in the affected schools," James Rodehaver, head of UNAMA's human rights unit, told AFP this week.
"UNAMA has made public its concerns about the use of torture in selected NDS facilities throughout the country, including Takhar, as a means to force persons suspected of insurgency activities to confess," he said.
"It is also very concerning that NDS publicised the confessions of the suspects in the Takhar case, including of the two schoolgirls. This violates fair trial rights, including the presumption of innocence, of the accused."
If it is shown that the confessions were forced, it is the duty of the courts to throw the confessions out as evidence, Rodehaver said.
The government denied that the suspects had been tortured.
"This is absolutely wrong, no one was tortured," said interior ministry spokesman Sediq Sediqqi.
"These people were arrested with evidence and we have their confessions. In the Sari Pul case (last month) it was spray involved, and in Takhar it was mostly pills. We have that evidence."
The World Health Organisation says there is no forensic evidence of poisoning in the cases, which were first noticed in large numbers in 2008.
Mass hysteria, properly known as mass psychogenic illness, is "the most probable cause" of the mysterious ailments, it says.
The symptoms include sudden nausea, dizziness and mass fainting episodes in which the girls are rushed to hospital, only to recover soon afterwards.
The WHO says that out of 1,634 cases in 22 schools over the past four years, no deaths have been reported.
It adds that the outbreaks appear to follow a seasonal pattern, starting in April/May, close to the school examination period, but notes that "the diagnosis of mass hysteria is still contentious".
With no physical cause established, Robert Bartholomew, a sociologist and author, told AFP in May that the poisoning scares had "all the earmarks of mass psychogenic illness, also known as mass hysteria".
Bartholomew said he had collected more than 600 cases of mass hysteria in schools dating back to 1566 in Europe, "and the Afghan episode certainly fits the pattern".
"The tell-tale signs of psychogenic illness in these Afghan outbreaks include the preponderance of schoolgirls; the conspicuous absence of a toxic agent; transient, benign symptoms; rapid onset and recovery; plausible rumours; the presence of a strange odour; and anxiety generated from a wartime backdrop."
He noted there was a history of similar cases in combat zones, listing examples from the Palestinian territories in 1983 to Soviet Georgia in 1989 and Kosovo in 1990.
The Afghan incidents came "within a larger social panic involving the fear of Taliban insurgents", he added.
Afghanistan has been at war for the past 30 years, and according to the director of the government's mental health department, Bashir Ahmad Sarwari, half the population suffers from mental stress caused by the conflict.
The mass hysteria phenomenon is not well understood, however, and many in Afghanistan resist the idea of a psychological cause.
The Taliban have denied responsibility for any poisoning attacks on girls' schools, but their history makes them an easy target for officials searching for someone to blame.
Before the Islamists were toppled in a US-led invasion after the 9/11 attacks on New York and Washington, they were notorious for their brutal suppression of women.
But now, more than three million girls attend school, according to government figures.
The United States leads a NATO force of some 130,000 troops in Afghanistan, but they are due to withdraw by the end of 2014, raising fears among Afghans that recent gains in women's rights may be eroded.