Miss Kelly, one of several prominent Catholics in Gordon Brown's Cabinet, has told whips she will be in Brussels on 14 July, the day that the vote will take place.
The Transport Secretary has infuriated colleagues and some in Number 10 by refusing to vote for a key part of the Government's legislative programme because of her religious beliefs.
The Human Fertilisation and Embryology Bill contains several measures that Catholics feel uncomfortable about.
The Bill will allow the creation of animal-human embryos - created by injecting animal cells or DNA into human embryos or human cells into animal eggs - to be used in medical research and then discarded.
That has outraged Catholic leaders, who insist that hybrid embryos, known as "chimeras", be regarded as human and their mothers should be allowed to give birth to them.
However, under pressure, Mr Brown allowed a free, conscience, vote when the matters were debated in the Commons last month on condition that ministers would have to vote for the entire bill when it returned to the Commons.
That "deal" has been accepted by other Catholic Cabinet ministers including Des Browne, the Defence Secretary, and Paul Murphy, the Welsh Secretary. But Miss Kelly's determination to not be forced to vote for the bill has led to her citing a meeting in Brussels as a reason for her absence from the Commons on Monday week.
Some ministers have privately said that Miss Kelly should vote with the Government or stand down from her Cabinet post.
One MP said: "She would have a lot more respect if she voted with her conscience but accepted that as such she will have to pay the price and cease to be part of the Government. Of course as a backbencher she would not get £130,000 and a car."
A mother of four, Miss Kelly, 38, has been reported to be a member of Opus Dei, the Catholic organisation. When she was Communities Secretary and the Cabinet minister responsible for equalities policy, she was criticised by gay rights groups for refusing to say if she believed homosexuality was a sin.
Last night a spokeswoman for Miss Kelly said she going to Brussels for meetings on EU-wide transport issues as "it is something she has wanted to do for some time." Some of the discussion will be about green car tax measures including "new car CO2".
But colleagues have also expressed suspicion as normally MPs can return from Brussels in time for 10pm Commons votes. However, she will stay over night in Belgium.
Other Labour backbenchers have noted that she is often absent from votes on Monday. One has nicknamed her "the Boomtown Rat" as she "doesn't like Mondays."
Miss Kelly was said to be arguing within the Government last year for Catholic adoption agencies to be exempt from equality laws forcing them to offer children to adoption by gay couples.
Senior Catholics in the Whips Office like Tommy McAvoy and Frank Roy will vote for the Bill.
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