The dormitory held about 30 beds rammed in so close that there was hardly a breath of air between the bare metal frames. Apart from shrines and salutations to "Our Great Mother", the white walls were bare. The torch swept across the faces of children sleeping, screaming, laughing and sobbing, finally resting on the hunched figure of a boy in a white vest. Distressed, he rocked back and forth, his ankle tethered to his cot like a goat in a farmyard. This was the Daya Dan orphanage for children aged six months to 12 years, one of Mother Teresa's flagship homes in Kolkata. It was 7.30 in the evening, and outside the monsoon rains fell unremittingly.

Earlier in the day, young international volunteers had giggled as one told how a young boy had peed on her while strapped to a bed. I had already been told of an older disturbed woman tied to a tree at another Missionaries of Charity home. At the orphanage, few of the volunteers batted an eyelid at disabled children being tied up. They were too intoxicated with the myth of Mother Teresa and drunk on their own philanthropy to see that such treatment of children was inhumane and degrading.

Mother Teresa founded the Missionaries of Charity in 1950 in Kolkata, answering her own calling to "serve the poorest of the poor". In 1969, a documentary about her work with the poor catapulted her to global celebrity. International awards fol-lowed, including the Nobel Peace Prize and a Congressional Gold Medal. But when, in her Nobel acceptance speech, she described abortion as "the greatest destroyer of peace today" she started to provoke controversy. She died on 5 September 1997, her name attached to some 60 centres worldwide, and India honoured her with a state funeral. Her seven homes for the poor and destitute of Kolkata, however, are her lasting monument.

I worked undercover for a week in Mother Teresa's flagship home for disabled boys and girls to record Mother Teresa's Legacy, a special report for Five News broadcast earlier this month. I winced at the rough handling by some of the full-time staff and Missionary sisters. I saw children with their mouths gagged open to be given medicine, their hands flaying in distress, visible testimony to the pain they were in. Tiny babies were bound with cloths at feeding time. Rough hands wrenched heads into position for feeding. Some of the children retched and coughed as rushed staff crammed food into their mouths. Boys and girls were abandoned on open toilets for up to 20 minutes at a time. Slumped, untended, some dribbling, some sleeping, they were a pathetic sight. Their treatment was an affront to their dignity, and dangerously unhygienic.

Volunteers (from Italy, Sweden, the United States and the UK) did their best to cradle and wash the children who had soiled themselves. But there were no nappies, and only cold water. Soap and disinfectant were in short supply. Workers washed down beds with dirty water and dirty cloths. Food was prepared on the floor in the corridor. A senior member of staff mixed medicine with her hands. Some did their best to give love and affection - at least some of the time. But, for the most part, the care the children received was inept, unprofessional and, in some cases, rough and dangerous. "They seem to be warehousing people rather than caring for them," commented the former operations director of Mencap Martin Gallagher, after viewing our undercover footage.

I first learned of the plight of the Kolkata children from two international aid workers, both qualified nurses and committed Catholics. They came to me after working as volunteers for the Missionaries of Charity last Christmas. Both made the comparison with images that emerged from Romanian orphanages in the early 1990s after television news teams first gained access.

"I was shocked. I could only work there [Daya Dan] for three days. It was simply too distressing. . . We had seen the same things in Romania but couldn't believe it was happening in a Mother Teresa home," one told me. In January, she and her colleague had written to Sister Nirmala, the new Mother Superior, to voice their concerns. They wrote, they told me, out of "compassion and not complaint", but received no response. Like me, they had been brought up in Catholic schools to believe that Mother Teresa was the holiest of all women, second only to the Virgin Mary. Our faith was unwavering, as was that of the international media for about 50 years. Even when the sister in charge of the Missionaries of Charity's Mahatma Gandhi Welfare Centre in Kolkata was prosecuted and found guilty of burning a young girl of seven with a hot knife in 2000, criticism remained muted.

The most significant challenge to the reputation of Mother Teresa came from Christopher Hitchens in 1995 in his book The Missionary Position. "Only the absence of scrutiny has allowed her to pass unchallenged as a force for pure goodness, and it is high time that this suspension of our critical faculties was itself suspended," he wrote, questioning whether the poor in her homes were denied basic treatment in the belief that suffering brought them closer to God. Hitchens's lonely voice also raised the issue of the order's finances, which in 1995 (and still in July 2005 when we were filming) seemed never to reach Kolkata's poorest.

Susan Shields, formerly a senior nun with the order, recalled that one year there was roughly $50m in the bank account held by the New York office alone. Much of the money, she complained, sat in banks while workers in the homes were obliged to reuse blunt needles. The order has stopped reusing needles, but the poor care remains pervasive. One nurse told me of a case earlier this year where staff knew a patient had typhoid but made no effort to protect volunteers or other patients. "The sense was that God will provide and if the worst happens - it is God's will."

The Kolkata police force and the city's social welfare department have promised to investigate the incidents in the Daya Dan home when they have seen and verified the distressing footage we secretly filmed. Dr Aroup Chatterjee, a London-based Kolkata-born doctor, believes that if Daya Dan were any other care home in India, "the authorities would close it down. The Indian government is in thrall to the legacy of Mother Teresa and is terrified of her reputation and status. There are many better homes than this in Kolkata," he told us.

Nearly eight years after her death, Mother Teresa is fast on the way to sainthood. The great aura of myth that surrounds her is built on her great deeds helping the poor and the destitute of Kolkata, birthplace of her order, the Missionaries of Charity. Rarely has one individual so convinced public opinion of the holiness of her cause. Her reward is accelerated canonisation.

But her homes are a disgrace to so-called Christian care and, indeed, civilised values of any kind. I witnessed barbaric treatment of the most vulnerable.

The Missionaries of Charity have said that they welcome constructive criticism, and that the children we saw were tied for their own safety and for "educational purposes". Sister Nirmala even welcomed our film: "Our hopes continue to be simply to provide immediate and effective service to the poorest of the poor as long as they have no one to help them . . . May God bless you and your efforts to promote the dignity of human life, especially for those who are underprivileged."

For too long Mother Teresa's Missionaries of Charity have been blessing critics, rather than addressing justified and damning condemnations of the serious failings in their care practices.

Donal MacIntyre is a reporter and documentary-maker for Channel 5 Television