The report, signed by Security Minister Fahrudin Radoncic, was written in August and refers to the situation in 2012. The House of Representatives is due to discuss it on Thursday.
Economic crimes pose a big problem and are believed to have defrauded the state of more than EUR 30 million last year.
The Bosnian Security Ministry says there is evidence that criminals have "drilled through" state institutions and police structures, using bribes to obtain information on investigations against them.
"Most criminal groups have entrenched themselves in various structures and levels of government," the report says, adding that the Intelligence and Security Agency has such information.
The report says that 2012 saw 1.6 per cent less crimes than 2011. Crimes motivated by religious or national hate dropped 66.6 per cent, but human trafficking went up 25%. Corruption-related cases jumped 14.3%.