While pro-choice campaigners welcomed the move, the Society for the Protection of Unborn Children (SPUC) Scotland fiercely opposed the policy change and is reportedly consulting lawyers.
Chief executive John Deighan branded the decision "highly irresponsible" and claimed ministers may have "recklessly exceeded their powers".
Christian charity CARE also condemned the "significant policy shift" and said it raised huge concerns for women's safety and mental wellbeing.
Nola Leach, CARE's Chief Executive said in a statement: ""For the Scottish Government to make a policy change of this magnitude without any parliamentary scrutiny or public consultation is deeply concerning."
"Encouraging women to have abortions at home is extremely worrying. There will be no health care support on hand should something go wrong."
"The Scottish Government should do much more to provide real alternatives to abortion for those facing crisis pregnancies. It should properly fund those organisations which are seeking to provide such alternatives for women."
Scotland's Chief Medical Officer, Dr Catherine Calderwood, recently confirmed she had written to all health boards north of the border to say that the drug misoprostol could be taken by women outside a clinical setting.
Dr Calderwood said it was ''significant progress'' that women in Scotland who are up to nine weeks pregnant could take the second dose of the drug at home if they wanted, saying this would allow them "more privacy, more dignity''.