Rev Dr Iain Greenshields said the Presbytery of Dunfermline "abhorred" the actions of someone who laid out strips of bacon on a door handle at Dunfermline Central Mosque and on the doorstep.
Dr Greenshields said: "Over the last few years we have worked alongside our Muslim neighbours to foster a spirit of co-operation and mutual respect.
"We believe much of this [the intolerance] is sparked by social media and belongs only to a small minority who themselves have no strong or personal religious convictions."
Dunfermline Central Mosque called the incident a "deliberate symbol of hatred chosen as Muslims and Jews do not eat pork."
It also attributed the act to "hatred driven via social media" but acknowledged that only a minority of people in the area would endorse such behaviour.
"Its a shame that a minority within society want to only promote hatred and fear, who refuse to engage and get to know us, but we do recognise it is just a minority of people with this hatred of others," the mosque said in a Facebook post.
Dr Greenshields said the Church will write a letter to all schools in the area urging them to teach against social media hate campaigns during their assemblies.
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