In a letter to The Catholic Herald newspaper she said she was "saddened" that the paper was "obsessed" with abortion issues.
Ms Short said the paper seemed little interested in " improving living conditions for the one in four of the human family that live in abject poverty".
The letter was an attempt by the minister to defend her department's work in funding projects designed to cut unwanted pregnancies in the Third World.
The paper responded to Ms Short's comments calling them "a disgraceful slur" and accused the minister of being ideologically driven.
Preventing unsafe abortions
Ms Short added: "One of the reasons we fund such work is to ensure that more effective contraceptives are available to help reduce abortion.
"Around 75,000 women die each year from unsafe abortions.
"I believe that our work is doing much more to reduce abortion than are those who use your columns to try to prevent poor women in developing countries having access to contraception.
"It is a lack of access to contraception that is the cause of most of the abortion that still takes place in the world."
Although Ms Short was educated at a Catholic school and has described herself as an "ethnic Catholic" it is not the first time she has criticised the church's stance on abortion.
Earlier in the year she told The Guardian newspaper there were "reactionary forces" in The Vatican which were "deeply unholy" as their policies, if implemented, would lead to more people with the HIV virus and more women dying as a result of illegal abortions.
She said: "That is the position they are trying to work for. And it's a morally destructive course."
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