From Historical and Statistical Account of Dunfermline by Rev. Peter Chalmers Vol. 1 

As the civilized Pagan nations, Greeks, Romans, &c., considered it unlawful to bury their dead within the precincts of their cities, lest their sacred places should be defiled, and generally interred them in the suburbs, and the sides of the highways, the early Christians followed the practice.  But in the fourth century, from a mistaken feeling of piety, an attempt was made by them to have their churches used as repositories for their dead, especially for such as had been of eminent Christian reputation.  This was resisted by the Emperor Theodosius in that century, who issued an ordinance, that all who should be guilty of this practice “should be fined in one-third part of their patrimony.”  From the superstitious notion,  however, that interment in a place of sanctity would be beneficial to the souls of the deceased, aided by the introduction of the Popish tenet of worshipping and doing homage to the dead and their relics, as well as from the idea of its being a great honour to be buried within a church or chapel, or near an altar, the custom of so burying became almost universal among the great, and all who could afford to purchase the privilege.  In the thirteenth century and afterwards, it was much prized by the Roman Catholic population, and the once-lettered pavement of our old church, of which some remains still exists, show the prevalence of the custom.

Soon after the Reformation, the Church of Scotland saw the evils of the custom not only in a religious point of view, but as regarded the health, comfort and convenience of the living, and sought to put an end to it. 

As early as 24^th October 1576, a question was proposed in the General Assembly, as to its propriety.  Sessio 7. “Whither if burrials sould be in the kirk or not?  Ansuerit.  Not ; and that the contraveiners be suspendit frae the benefites of the kirk, quhill [till] they make public repentance.”   The enactment, however, does not seem to have been always strictly observed ; for in the General Assembly held in April 1577, there is this record

Sessio 9a. “Anent the complaint made be David Fergusone vpon Mr James M’Gill, Clerk of Register, to the zong Laird of Rossyth, that agains the actis of the Kirk  they causit burie the vmquhill Laird of Rossyth in the Kirk of Dumferling, albeit the said David made them foirsein of the said act.   The kirk ordainit Johne Durie to warn the Clerk-Register to answer heirto, the first of May nixt to come.”* “The Clerk-Register beand present, declareit that the Proveist and Baillies of Dumfermling agriet to burie the said Laird of Rossyth in the Kirk ; that he was not the cause thereof, submit and himselfe allwayes to the judgement of the Kirk, if any offence be found done by him.” – Booke of the Universall Kirk of Scotland, Ban. Club Edit., Part 1., pp. 378,388 (1839).* Nearly a hundred years after this, an unseemly affray took place in the church-yard, by an attempt to inter another Laird (Stewart) of Rosyth within the kirk, which is thus recorded in the session minutes. The affray is remarkable for the very early hour at which it took place, and the fidelity and alertness of the then ministers in being at their post to oppose the meditated interment, by a forcible entrance into the kirk, and which even a writer was brought from Edinburgh to render legal :- * “24th April 1660. – The act and instrument following, being produced this day, Mr Rot. Kay, and Mr Wm. Oliphant, present ministers of the kirk of Dunfermline, desirit y^t it my^t be insert in the session-book for y^r exoneration, which was consented to be the session.  Off the qlk act and instrument the tenor follows:-* “At Dunfermline, the 20 day of Aprile Jajvi^c and thrie score yeirs – ““The w^ch day, in presence of me, notar publick, and witnesses, efter-nait compeirit ps~nlie at the kirk-dore of Dunfermline – betwixt 4 and 5 hours in the morning, Mr Ro^t. Kay, and Mr W^m. Oliphant, ministers, y^r who declaired, they were certainlie informed y^t the friends and kinsmen of the Laird of Rossyth, deceist, were of intention to bring the corps of the s^d laird w^thin the s^d kirk of Dunfermline, and y^t the keys of the kirk-dores were not in the kirk-officer’s hands, but had bein taken fra him yetngt.  And y^rfore did send and direct y^r kirk-officer to Ro^t. Walwood bailie of the s^d bru^t (who had taken the keys fra him, as they were informed), To desire and require him to give bak the keys of the s^d kirk-door, y^t they might have y^m in y^r custodie, who accordinglie went, and made report of his comission thus ; that the bailie said he had not the keys for the present, but had left y^m wth the toun-officer, that he might open the dore this morning to ring the 5 ho^r bell. Thairfor, beore 5 o’clock came, Johne Laurie, officer, w^th the keys, fra whome the sds Mr Rot. Kay and Mr W^m Oliphant demandit the s^d keys, w^ch he altogedder refusit, saying y^t y^r w^th he was to open, the dore to ring the 5 ho^r bell. And, in the meantyme George Carmichell srvito^r to the Laird of Buchanan, and Alex^r. Crookshank, writer in Edinburgh, came to the kirk-dore, at whom the s^d minister desyred to know y^r erand y^t tyme of day? Who ansred y^t they intendit to keip ye Laird of Rossyth’s old buriall-plaic.  To the which it was replyed by the ministers, y^t all burying w^thin the kirk was discharged be the General Assemblie in August 1643. And y^t y^r hade nevir bein any in this kirk since y^t tyme. And desyrit y^m to forbear fra breaing the kirk-floore, and burying w’hin the kirk. Which they wilfullie refused.  And wth 5 or 6 men thrust y^mseles in at the kirk-dore.  Q^rvpon, and vpon the refusal of the sd toun-officer to delyver they keys in manner foirsaid ;  And all and sundrie the premisses, the saids Mr Ro^t. Kay, and Mr W^m. Oliphqnt, ministers, askit act and instrument, ane or mae, in the hands of me, notar-publict, under subcrywand ;  And protestit y^t as they were frie, and had no accession to the sd irregular fact, so they my^t be frie fra all the evills and consequents y^t my^t follow y^rvpon.* “Thir things were done day, yeir, and plaic foresaid, betwixt 4 and 5 ho^rs in the morning. Before James Marshall, Patrik Anderson, Archibald M’Craich, burgess [es] of Dunfermline ;  George Befrage, srvitor to the s^d Mr W^m. and Arthere Kay, sons lau^ll to the sd Mr Ro^t, witness [es] to the premisses called and requyred, sic subscribitur.  I, henrie elder, notar-publict, Doe testifie and declare the haill premisses before set doun to be trewlie done, as is above exprest, be this my subscription usuall, H. Elder.  Quhilk act and instrument being red, Peter Walker, Provost, declairs y^t they medled w^th no keys bot y^t which properly belonged to the toun.  And desyred this to be marked.”

There was published in 1610, 4to, an interesting book entitled “The Blame of Kirke-Buriall, tending to perswade Cemiteriall civilitie, by Mr William Birnie, minister of Lanark.”  “First preached,” it is added on another page, “then penned, and now at last propyned to the Lord’s inheritance in the Presbyterie of lanerk by Mr W.B. the Lord his minister in that ilk, as a pledge of his zeale, and care of that reformation. Matth. Viii.22.”  This book was reprinted by the Bannatyne Club in 1834, edited by W.B.D.D. Turnbull, Esq. Advocate.