Claims by Mr Howard that Pakistan is a "safe" country and therefore its citizens are unlikely to deserve asylum in Britain are contradicted by Mr Rifkind in a letter obtained by The Independent.
Writing to Brian Mawhinney, chairman of the Conservative Party, Mr Rifkind states that there are credible reports of persecution and attacks, backed by the authorities, against a minority religious group in Pakistan.
Tomorrow the Commons willvote on the establishment of a "white list" of seven countries from where asylum applications would be presumed to be unsound unless it could be proved otherwise. The countries identified by the Home Office earlier this year during the second reading of the Asylum and Immigration Bill as "safe" are Cyprus, Poland, Romania, Bulgaria, Ghana, India and Pakistan.
Labour yesterday seized upon Mr Rifkind's letter as evidence of a rift between the Foreign Office and Home Office and is demanding the removal of Pakistan from the "white" list.
Amnesty International, the Refugee Council and other organisations say that people from countries on the list are in danger of persecution, torture and even death for their political and religious beliefs.
Mr Howard has defended the list as part of an attempt to reduce the number of economic migrants entering Britain.
But in May Dr Mawhinney, believed to be writing on behalf of a constituent, asked Mr Rifkind about the plight of the Ahmadis religious group, who under threat of death have been banned from declaring themselves to be Muslims in Pakistan.
Mr Rifkind replied: "Radical sectarian groups and individuals have carried out attacks against Ahmadis. In some cases there are credible reports that the local authorities have given tacit support to these actions.
"We, and our EU partners, have expressed concern to the government of Pakistan about the treatment of minorities and blasphemy laws. We understand that the government of Pakistan would like to amend the blasphemy laws, but they have encountered strong opposition to any changes and none has yet been enacted."
The last paragraph appears to contradict a Home Office assessment that "Ahmadis are recognised as a minority religious group and rights are safeguarded under the constitution".
Doug Henderson, a Labour home affairs spokesman, said: "This letter makes clear more divisions in the Conservative Party. I am making representations to the Secretary of State to have Pakistan removed from the list."
A Home Office spokesman said people from white-list countries with a genuine case would be confirmed as refugees.Reuse content