He told The TES Labour would not seek to change the long-established right of church schools in the state sector to use interviews with parents or pupils to determine whether they have a suitable religious commitment.
But he pledged to take a firm line with any church school found to be breaching guidelines which forbid them from selecting on grounds such as ability or background.
His commitment could lead to a head-on clash between an incoming Labour administration and the London Oratory, the Roman Catholic grant-maintained boys' school attended by the eldest son of party leader Tony Blair.
Last year, the Oratory's admissions procedures were queried by the Westminster church diocese which claimed it used interviews to choose pupils in breach of the Department for Education and Employment's guidelines.
The school has attracted controversy because it uses interviews to assess whether the aims, attitudes, and values of the parents and boys are in harmony with the school. As a result, it has taken pupils from as far away as Hertfordshire and Kent.
In September, the Education and Employment Secretary, Gillian Shephard, withdrew a previous instruction to the school to comply with the regulations following discussions with the head, John McIntosh. The U-turn came just a week after Prime Minister John Major indicated he wanted to change the rules to allow GM schools to determine their admission procedures.
Mr Blunkett insisted any action taken against church schools found to be contravening guidelines would have no bearing on the choice of school by Mr Blair and his wife Cherie, a practising Catholic, because their choice had been on religious grounds.
Earlier, he told the conference that Labour would end selection by interview. "We do not believe that parents should be vetted by head- teachers before children are admitted into their schools. We do not believe schools should choose pupils, but we believe parents' wishes should be respected.
"No one can tolerate the head of a school determining a child's place by the background of the parents."