The report said that 798 registered sex offenders are currently in custody
About one in 10 of all Scottish prisoners is a registered sex offender, according to figures released by the Scottish government.
Nearly 800 sex offenders were in jail at the end of March, out of a total prison population of about 8,000.
The data also showed 44 sex offenders in the community had been charged with a further sexual or violent offence.
Justice Secretary Kenny MacAskill said Scotland was leading the world in its approach to managing sex offenders.
The figures come from the Multi-Agency Public Protection Arrangements (Mappas), which came into force in April 2007, and mean the police, the Scottish Prison Service and councils jointly assess and manage sex offenders in the community.
The report for 2008-09 said that by the end of March, 2,967 registered sex offenders were living in Scottish communities with a further 798 in custody.
Those living in the community must register their movements and breaches of the requirement count as a further offence.
The latest report shows that last year the number of breaches was down on the previous 12 months.
However, 44 offenders were charged with a further sexual or violent crime, compared with nine the previous year.
The Scottish government insisted the figures were misleading as they were not a "like-for-like" comparison.
But Conservative justice spokesman John Lamont said there was "little to smile about" in the statistics.
He called for lie-detector tests for sex offenders, as well as GPS tracking and for those who abscond to be "named and shamed".
Labour's Paul Martin said: "The increase in the numbers caught reoffending is very worrying and action needs to be taken to tighten up procedures and assessments."
Robert Brown, justice spokesman for the Liberal Democrats, called the latest figures "the tip of the iceberg".
He said only one in ten recorded rape cases went to court and the rehabilitation in prison of sex offenders had "serious failings".
However, Justice Secretary Kenny MacAskill said: "The sad reality is that sex offenders and the threat they pose have existed for all of human history but what has improved is the way in which they are managed.
"Since devolution, three expert reviews and a cross-party inquiry have led to significant reforms to how these individuals are managed and only last month, Tayside Police began a pilot project that will entitle parents to know if a sex offender has access to their children."
He said Mappas had strengthened how the authorities worked together.
"While it is clearly worrying when any sex offender reoffends, it is encouraging that the reoffending rate last year equates to one in 68 when the general reoffending rate is far higher," Mr MacAskill said.