Cardinal Keith O'Brien has urged Catholics to withhold their vote from pro-abortion politicians, calling the practice an "unspeakable crime".
In an emotive but carefully worded statement, he warned Catholic politicians of "the barrier such co-operation erects to receiving holy communion".
Most commentators are taking the phrase as a thinly veiled warning politicians who do not oppose the practise could not expect to remain full members of the Catholic church.
The sermon, delivered at St Mary's Cathedral in Edinburgh, marked the 40th anniversary of the Abortion Act.
"I urge politicians to have no truck with the evil trade of abortion. For those at Westminster this means finding means of overthrowing the legislation, which makes the killing possible," he said.
"For those at Holyrood that means refusing to allow our health services to participate in the wanton killing of the innocent."
Abortion is still legislated by Westminster, but the Scottish government is committed to reducing the number of unintended pregnancies through their Respect and Responsibility sexual health strategy.
Cardinal O' Brien continued: "Let us build up within our society a generation of medical professionals who are unwilling to co-operate in the slaughter.
"I call on our universities and medical schools to teach that all human life deserves protection.
"I call on all politicians to answer one simple question: will you protect the right to life of all persons in our society from conception until natural death?
"And I call on you to hold these elected representatives to account.
"For those unwilling to give this support we must be unwilling to give our vote," he said.
The sermon instantly provoked a storm of protest. Critics argued elected representatives should be free to exercise their judgement without threats from church leaders.
Jeremy Purvis, a Liberal Democrat member of the Scottish parliament, accused the cardinal of using "inflammatory" language.
Ann Furedi, the chief executive of the British Pregnancy Advisory Service (BPAS), a leading sexual health charity which provides over 55,000 women a year with abortion care, claimed there are many in the Catholic church who do not share the cardinal's views.
"At BPAS, we offer a non-judgemental service. We see many couples and women for contraception and abortion treatment who are active Catholics. It is quite clear that not everyone sharing the Catholic faith with the cardinal agrees with him on this issue," she said.
"The cardinal has every right to hold his views. He obviously doesn't have to have an abortion, or provide one."
She continued: "Abortion is a safe, legal and medically legitimate procedure, essential in safeguarding women's reproductive health. Women should be able to make their own choices about their bodies and their future."