New figures show there were arrests for sectarian offences in all of Scotland's 32 authorities, and while 40% of all charges were in Glasgow, religiously aggravated offences have more than doubled in Edinburgh in the past year.
The Crown Office and Procurator Fiscal Service (COPFS) said the overall hike may be partly due to increased awareness, reporting and recording of such crimes, following several incidents that received public attention the previous year.
Anti-sectarian charity Nil By Mouth said the 6000 arrests for sectarian offences since 2003 show "this problem goes far beyond football and Facebook".
The number of charges in football stadiums decreased from 90 to 67, just 8% of the overall total, while football-related offences made up less than one- third of all charges.
Just 2% of incidents, 18 charges, took place at a parade.
In all, there were 876 charges with a religious aggravation reported in 2011-12, compared with 693 charges in 2010-11, an increase of 26%. Of these, in 58.1% of occasions the religion targeted was Catholicism, while 40.3% of incidents were directed at those perceived to be Protestants.
The Catholic Church said there had to be a "public acknowledgement of the extent of anti-Catholicism in Scotland".
Archbishop Philip Tartaglia, President of the Bishops' Conference of Scotland, said; "Sadly, it seems incontrovertible now that our problem is not so much sectarianism but anti-Catholicism."
Nil By Mouth campaign director Dave Scott said: "The Government is piloting work in prisons at the moment and we would urge ministers to ensure a rehabilitation package is made compulsory for anyone convicted of sectarian offences."
According to the COPFS figures, the police were victims of religious abuse in more than half (51%) of the charges and were the most common target, the same as last year. Workers, such as hospital staff, security staff and taxi drivers, were targeted in 13% of incidents.
This, according to the Scottish Government report, "suggests that for the majority of charges it is unlikely the accused knew the religious affiliation/belief of the victim at the time of incident".
The Government has warned the figures provide "an indication but not a comprehensive picture of the prevalence of religiously offensive conduct in Scotland" and that sectarian offences are often reported to COPFS as racial rather than religious aggravations.
Some 93% of the accused were male and 58% were aged between 16 and 30. More than half of all charges were alcohol-related.
There were 19 attacks on Islam, up from 15, and 14 on Judaism, down from 16. More than one-quarter of anti-Islam charges were for assaults.
Minister for Community Safety Roseanna Cunningham said: "These figures show that as well as tough enforcement, we need to tackle the root causes of religious prejudice that sadly is all too prevalent in parts of Scottish society."