A note handed to some worshippers in south Wales urged people not to make "heroic" efforts to attend if unwell.
But a church spokesman said a priest should speak to a congregation rather than give written instructions and only when he "feels that he has to do so".
He said church advice would be based on that from the assembly government.
Wales has 71 confirmed swine flu cases but will not be part of the National Pandemic Flu Service (NPFS) being launched in England on Thursday.
Health Minister Edwina Hart has said Wales is "well behind the curve compared to areas of England" for the number of swine flu cases.
The National Public Health Service for Wales estimated around 1,335 people had contacted their GP to complain of flu-like symptoms, but not necessarily swine flu, in the week to 5pm on Saturday 18 July.
Some worshippers in the south Wales diocese of Menevia attending mass on Sunday had been given a note advising them not shake hands during services in order not to risk spreading the swine flu virus.
The note advised churchgoers to make a small bow when saying "peace be with you" during mass rather than offer a handshake that "may be refused".
The diocese includes Swansea, Neath, Cardigan, Pembrokeshire, south Powys and Carmarthenshire.
But a diocesan spokesman said it had been left to parish priests individually to advise congregations on "standard instruction for any illness" as they deemed it appropriate.
He said there had been "no instruction from the bishop" and advice should have been given verbally rather than being printed out.
He added: "It's causing a bit of a panic if it's written down when it shouldn't have been."
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Source (BBC)
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