More than 2,000 Catholic schools were told by their Church yesterday that it would be "unwise" to seek academy status.
This is a setback for the Education Secretary, Michael Gove, who has written to every school in England urging them to apply for the status.
The Catholic Education Service for England and Wales advised schools to use "great caution".
Under the Government's proposals, the land and property of the school would transfer from the diocese to the new trust running the academy.
But Oona Stannard, chief executive of the Catholic Education Service, said: "Trustees are unlikely to give their permission.
"Therefore, a school wanting to become an academy might effectively become homeless."
Meanwhile, Mr Gove said yesterday that a total of 1,700 schools had applied for academy status since the letter had been sent out.
Schools rated as "outstanding" by Ofsted, the education watchdog, will automatically be approved for academy status.