The guidance has been developed with the UK Border Agency and has the backing of Immigration Minister Damian Green.
It advises clergy not to publish banns for marriages involving people from a non-European country national.
Instead, they should direct the couple to apply for a common licence, which involves the swearing of affidavits and requires the couple to provide proof of identity and address, receive visits from the vicar, and attend wedding preparation classes.
Clergy who suspect that a marriage is not genuine are being told they must make their concerns known to the person responsible for granting the licence at the diocesan legal office.
Diocesan legal officers should be told "immediately" if the couple insist on having banns read rather than applying for a common licence.
In such a case, the couple would be required to provide verifiable evidence of their right to marriage by banns, such as a driving licence and official correspondence, and would have to be visited by the vicar at the address provided.
The guidance makes clear that clergy who refuse to carry out a marriage on the grounds laid out in the guidance will not be considered guilty of misconduct.
Clergy are also advised to contact police if they are threatened for refusing to conduct a marriage they have suspicions about.
The Bishop of of Ripon and Leeds, the Rt Rev John Packer, said: "The House of Bishops is clear that the office of holy matrimony must not be misused by those who have no intention of contracting a genuine marriage but merely a sham marriage.
"The purpose of this guidance and direction from the bishops to the clergy and to those responsible for the grant of common licences is, therefore, to prevent the contracting of sham marriages in the Church of England."
Immigration Minister Damian Green said the UK Border Agency was working very closely with the Church of England in investigating and disrupting suspected sham weddings, as well as in providing advice and support.
"The new guidance being launched today by the Church of England is another step in the right direction in tackling these abuses," he said.
"Increasing enforcement action has resulted in 155 arrests across the country and would-be fraudsters should remember that a marriage itself does not equal an automatic right to remain in the UK."
The Rev Alex Brown, 61, was jailed for four years last September for conducting hundreds of sham marriages between African men and Eastern European women at the Church of St Peter and St Paul in St Leonards-on-Sea, East Sussex.
The BBC said 155 people had been arrested in the UK over the past nine months as a result of investigations into church and civil ceremonies.