While there was an overall reduction in racial and religious hate crime in 2012/13, statistics show a rise in anti-Islamic charges and those relating to disabled people, compared with 2011/12.
The figures were revealed in a series of reports on hate crime, religiously aggravated offending and the first annual statistics from the Offensive Behaviour Act.
Charges where conduct was derogatory towards Islam totalled 80 in 2012/13 compared with just 19 the previous year, however 57 of these were from one event, the Campaign to Welcome Refugees march in Glasgow, where there was a counter demonstration by the Scottish Defence League (SDL).
The figures were published as Alex Salmond held talks with representatives of the Muslim Council, where they discussed the latest findings and the First Minister reaffirmed the Scottish Government's commitment to tackling racial and religious hatred and all forms of prejudice.
The number of charges reported against disabled people was more than double the previous year at 138, while the number of charges related to sexual orientation was 12% higher than the previous year.
The rise was attributed to the introduction of the Offences (Aggravation by Prejudice) (Scotland) Act in March 2010, which specifically addresses prejudice relating to disability, sexual orientation and transgender identity and may have led to increased reporting of such offences.
Overall, the reports showed there has been a 15% reduction in offences involving religious hatred on the previous year, while charges for race crime have fallen by 12% to 4,012.
Community Safety Minister Roseanna Cunningham said: "Any form of attack or discrimination based on the assumption of someone's religion, race or cultural background is completely unacceptable.
"While the decrease in both racist and religiously aggravated offending are to be welcomed, it is concerning to note the rise in charges directed towards the Islamic community and towards those with disabilities.
"Scotland is a country which does not tolerate racial or religious prejudice and we are a nation where people of all faiths and none can live in peace. This is borne out by today's figures - we are not becoming more intolerant as a society, but we are becoming less tolerant of those who hold prejudiced beliefs.
"The firm action taken against the SDL and what appears to be increased reporting of crimes against people on the basis of disability or sexual orientation confirms that zero tolerance approach."
The first statistics on the Offensive Behaviour at Football and Threatening Communications (Scotland) Act 2012 were also published today, revealing there were 268 charges of "offensive behaviour at regulated football matches" in the first full year, 2012/13. The majority of charges were at football stadia.
"The statistics from the first year of the Offensive Behaviour Act show that strong action is being taken to tackle the actions of the small minority of fans who indulge in offensive behaviour at football," Ms Cunningham said.
"However, it is clear that the vast majority of fans are well-behaved and a credit to Scotland's national game."
Commenting on the reports, Lord Advocate Frank Mulholland QC said: "It is encouraging to see a 12% drop in charges motivated by racial prejudice and a 15% reduction for criminality involving religious hatred. There is no place for complacency and I hope the downward trend continues in the coming years.
"What I do find concerning is the rise in offences committed against individuals because of their sexual orientation. I hope that this is the result of the increased confidence in reporting which has encouraged more people to report this type of offending, but it is something we will closely monitor and explore ways we can look to reducing such offending, as we have done with other forms of hate crime."
Dave Scott, director of anti-sectarianism charity Nil By Mouth, said: "It's pleasing to see a reduction in the number of arrests from last year but the figures once again prove we still have someway to go to rid Scotland of this poison.
"Over the last decade there have been over 7,000 people charged with religious hate crimes and with under-30s accounting for 50% of the total number of offences, this has to be the generation on which we focus our efforts."
He called for a mandatory rehabilitation programme for anyone convicted of a sectarian offence.
The Conservatives said the new figures from the Offensive Behaviour Act demonstrated it was "legislation for legislating's sake".
The party opposed the Act when it was passed at Holyrood, arguing there were already sufficient laws in place to deal with this type of offending.
Tory MSP John Lamont said: "Today's statistics show that while 250 people have been charged under the new sectarian law, this has resulted in an almost identical fall in comparable breach of the peace charges.
"And since only a small number have been convicted under the section dealing with threatening communications, it raises major questions of why this legislation was ever passed.
"The fact is, this Bill has done more harm than good, and is yet another example of the SNP legislating for legislating's sake."
Labour's Jenny Marra said: "The flawed legislation that the SNP pushed through is only being used for a minority of cases. Labour is calling for a review of this Act to see if it's actually working and useful in tackling sectarianism.
"Scottish Labour is committed to tackling sectarianism but the focus should be on working in our communities to tackle sectarianism at its roots."