The number of charges linked to race, religious aggravation, disability and sexual orientation all rose, the Crown Office and Procurator Fiscal Service said.
The increase between 2010-11 and 2011-12 was explained in part by increased awareness of offences and a crack-down by prosecutors and police.
Lord Advocate Frank Mulholland QC said: "It is encouraging to see that many more of those subjected to such offences now have the confidence to report them.
"We will not tolerate bigotry and prejudice."
The figures do not include 42 charges reported to the Crown linked to a new law on religious sectarian hate crime at football matches, which came into force on March 1.
The number of charges linked to race crimes rose by 8% from 4178 to 4518, taking the total to a six-year high.
Religious crime charges increased by 29% from 695 to 897 in a year, the most since new legislation came into force through the Criminal Justice (Scot-land) Act 2003. More awareness after media attention prompted the "large increase", the Crown said.
Laws covering offences aggravated by sexual orientation, transgender identity and disability came into force on March 24 2010.
Charges relating to disability increased to 68 from 48 between 2010-11 and last year, while those linked to sexual orientation increased by 46% from 447 to 652.
There were 16 charges reported with an aggravation of prejud-ice to transgender identity, two more than the previous year.
Green MSP Patrick Harvie, who steered the Offences Aggravated by Prejudice Act through Holyrood, said: "The overall increase in all categories is troubling."
Community Safety Minister Roseanna Cunningham said: "The small minority who think that this kind of behaviour is somehow acceptable are finding out the hard way that it isn't."
Labour community safety spokeswoman Jenny Marra fears "these statistics, for the first time, begin to shine a light on the true scale of hate crime in Scotland".