The unit will work to crack down on attempts by gangsters to infiltrate local authorities and public-sector contracts.
Officers from the unit will offer advice to every public-sector organisation - including health boards, quangos, the prison service, the Scottish Government and local authorities - on how to avoid or protect against specific vulnerabilities to organised crime.
Using the experience of police counter-corruption squads, specialist officers have developed an "integrity framework" that identifies ways to protect staff against criminals trying to exert power or extort money from public bodies.
Public officials will be advised to look out for vulnerabilities among staff, including substance misuse, inappropriate associations and financial problems. Advice might also include more in-depth vetting procedures and random drug-testing for workers.
The unit will be made up of two teams, one to focus on preventing corruption within Police Scotland and a second team to focus on the public sector.
Detective Superintendent Sean Scott will lead the team that will focus on the public sector as well as investigating any individuals involved in corrupt activity.
Mr Scott said: "People are well aware of media exposés of corrupt practices in parts of the public sector. It has primarily been down south, but we are not immune to it up here. We have to ensure public money is not being misused or siphoned off.
"We are offering our own take on the integrity framework, with a focus on main threat areas, such as finance, procurement, personnel and an emphasis on putting the right people in the right jobs. We will be offering advice and expertise, not dictating what organisations do."
He added: "If staff are approached by organised criminals they need to know where to go and have the confidence to report it. Substance misuse is a known vulnerability because it can be used to coerce or threaten a person.
"We want to ensure that if people have any suspicion of corruption they report it. They can report it direct to us confidentially or go through their own organisation's helpline."
The move follows an investigation into alleged fraud and corruption at City of Edinburgh Council. Fifteen people, including four former employees, were charged last year in connection with alleged fraud at the council.
In 2009, NHS Greater Glasgow and Clyde, Scotland's biggest health board, went ahead with a £2 million contract with a taxi firm previously linked to serious organised crime, despite written and verbal recommendations from Strathclyde Police to stop the move.
The health board officially granted the tender to Network Private Hire following months of delays after the police took the unusual decision to intervene.
Organised crime is estimated to be worth £9.2 billion in Scotland. The UK sits 16th in the world rankings of perceived corruption, according to Transparency International.
Mr Scott added: "A big issue is the lack of intelligence. Transparency International looks at the perception of corruption. We need to know where it is happening across Scotland. We are not saying this is rife in the public sector. Corruption has been with us since time immemorial. Historically, some individuals in positions of power have abused that power."
Chief Constable Sir Stephen House said: "The actions of the few who engage in corrupt activity have a disproportionate impact on public confidence and the reputation of any public organisation.
"At a time of increasing budget constraints on the public purse, it is important we do all we can to protect the public sector and our communities.
"The move to a single police service in Scotland has presented us with an ideal opportunity to introduce consistency and co-ordination on a national scale but also the chance to work with our partners in the public sector to strengthen the barriers against corruption."