The girl was banned from lessons at Goldthorn Park primary school in Wolverhampton for the winter term. She was only allowed to return this year provided she was excluded from activities such as PE, breaktimes and school visits.
The governors ruled that the short-bladed kirpan, worn as a religious symbol, posed a threat to the safety of staff and pupils.
Their decision was taken shortly after the machete attack at the nearby St Luke's primary school in which pupils and staff were injured.
Local councillor Bob Jones suggested the governors had overreacted to the attack, coupled with a wider public concern over knife-related crime after the fatal stabbing of London headteacher Philip Lawrence.
Mr Jones, who is also chairman of the West Midlands police authority, said: "They have legitimate concerns, especially in the aftermath of St Luke's, but if they had done more research then their concerns would have been allayed. "
Many other schools in the country permitted Sikhs to wear the kirpan and had experienced no problems, Mr Jones said.
The governors were split on whether to formally exclude the girl and she eventually spent most of the winter term at home doing unsupervised school work, without having been formally excluded.
Chair of governors John Rowley said they preferred not to use their power to discipline her on "behavioural conditions" and instead to let the LEA send her to an alternative local school, but her father rejected this option. At home the girl did some supervised schoolwork, until shortly before Christmas when the school agreed to teach her in isolation. She has been taught under these conditions since the beginning of this month.
Previous attempts in Peterborough and elsewhere to prevent Sikhs carrying the kirpan have been thwarted by an exemption clause in the Offensive Weapons Act, according to the Sikh Missionary Society.
Spokesman Sarup Singh said: "This is an inappropriate and unlawful treatment of the child. I can only think that it is due to the insensitivity of the school to religious tradition."
The girl's father insists that she should be able to wear the kirpan, which is sewn into a sheath and strapped securely against the body. He has refused to sign an indemnity form holding him responsible inthe event of injury caused by the dagger.
Chairman of the governors, councillor John Rowley, said that the decision to remove the girl, who has an exemplary school record, was taken after the "emotive" attack on St Luke's primary school. But he said the main concern was the danger of the dagger getting into other hands.
He hoped the girl's father would accept the governors' indemnity proposal before the issue caused tension with the local Sikh community.
"We have a difficult task of balancing health and safety with religious beliefs and I hope for a solution before the issue becomes further polarised, " he said.