The founder of a controversial school that treats severely autistic and emotionally disturbed children by shocking them into submission with the use of electrodes has been forced to quit the institution and serve five years' probation.

Matthew Israel, a Harvard-trained psychologist, has created a treatment that is unique to the US and possibly the world. The Judge Rotenberg Center, just outside Boston, disciplines its students using a punishment machine that Israel invented called the GED, which gives a two-second electric shock to the skin of up to 90 milliamps.

At the centre, which was profiled by the Guardian earlier this year, students wear backpacks around the clock with the GED electric generators inside them, and are zapped using remote control devices controlled by their carers. In some cases, they are shocked as often as 30 times a day as a means of dissuading them from behaviour deemed dangerous to themselves or others.

The criminal charges brought against Israel relate to an incident in August 2007 at one of the school's residential homes where students sleep at night. A call came in from someone posing as an authorised supervisor, who informed the carers on duty that two teenagers had misbehaved and should be given shock treatment.

At 2am, the boys were strapped on boards and given multiple shocks. One of the boys, aged 18, was shocked 77 times over a three-hour period and the other boy, aged 16, was shocked 29 times. It was later discovered that the initial call had been a hoax.

The Massachusetts attorney general, Martha Coakley, indicted Israel over allegations that he ordered his staff to destroy video evidence that revealed exactly what happened that night. Prosecutors had previously ordered that the video recordings from the home were preserved.

"Dr Israel then attempted to destroy evidence of the events and mislead investigators, and that conduct led to his indictments today. Today's action removes Dr Israel from the school and should ensure better protection for students in the future," Coakley said.

The conviction is a substantial blow to Israel, who has weathered a storm of protest about his controversial methods for 40 years. He announced his retirement from the school on 2 May, without referring to the pending criminal case. He said he was moving to California, where his wife Judy lives.

"I am now almost 78 years old, and it is time for me to move over and let others take the reins," he said in a resignation letter.

But his departure will not materially change the way the school operates, crucially its technique of disciplining children by meting out electric shocks as a form of supposedly therapeutic punishment. Of the school's 225 students, 97 are currently on the electric shock regime.

The terms of the plea deal struck between Israel and the prosecutors require the school to introduce additional monitoring to prevent a similar lapse of security happening again. But the shocks themselves can continue.

"The case was only about Israel's conduct, it did not address the way the school is run," a spokesman for the attorney general's office said.

Laurie Ahern of Disability Rights International, which has been a persistent critic of the school, said that without an end to the shocks, Israel's departure would be irrelevant. "I don't see any radical change at the moment."

Hillary Cook, who spent three years at the school until 2009, and who was regularly shocked, said that whatever happened to Israel, she wanted to see the regime of shocks abolished. "I'm just worried about the kids who live there, because I know what it's like. They say the shocks are like a bee sting, and believe me they are not. It should be illegal to physically harm children and disabled people in this country."

The school has been a subject of huge controversy over past decades, with regular attempts to shut it down. Last year its use of electric shocks was attacked as a form of torture by the UN rapporteur on torture.

In February, the justice department opened an investigation into the school after it received a complaint alleging the centre had violated disability laws.

Despite the negative publicity directed at him, Israel managed to keep operating for so long partly because he had the vociferous support of parents of severely autistic children at the school.

The centre rarely uses drugs on its students, in contrast to many other homes for autistic people where heavy doses of psychotropic drugs are prescribed. At the time of Israel's resignation, Louisa Goldberg, whose son has been on the shock regime for the past 11 years, said that "Dr Israel's pioneering efforts have given our child back his life and we are extremely grateful for all that he has done for our family."