The Los Angeles-based movement, whose members include the films stars Tom Cruise and John Travolta, now faces charges following a ten-year inquiry.
Jean-Claude Van Espen, an investigating prosecutor, said up to 12 people, who have not been named, should be charged.
His investigation concluded that the church's Europe office, based in Brussels, and its Belgian missions, conducted unlawful practices in medicine, violated privacy laws and used illegal business contracts.
A spokeswoman at the Federal Prosecutors Office, said: "They also face charges of being ... a criminal organisation."
The church accused the prosecutor of hounding the organisation. A court will now decide whether to press charges against the Scientologists, who are expected to challenge the move when a hearing takes place in the next two to three months. This could delay the case for years.
Scientology has been active in Belgium for nearly 30 years and is seeking to expand in Europe.
It was founded in 1953, boasts ten million members and teaches that technology can expand the mind and help solve problems.
It came to the fore in Britain in May when John Sweeney, a BBC Panorama reporter, lost his temper in an on-screen shouting match with a member of the church.
In 2003, it opened an office a few yards away from the headquarters of the European Union to lobby for its right to be recognised as an official religious group, a status it does not enjoy in Belgium.
A Belgian parliamentary committee report in 1997 labelled Scientology a sect and investigations were launched into the group's finances and practices, such as the personality tests conducted on new members.
Investigators have spent a decade trying to determine how far Scientology went in recruiting converts after numerous complaints were filed with police by former members claiming they had been the victims of intimidation and extortion.
Justice officials seized financial records, correspondence, bank statements and other papers during the inquiry to track the flow of money to Scientology. Police also raided the offices of several consultancy firms linked to the church.
Some other European countries are hostile to Scientology, with the German government considering it a commercial enterprise that takes advantage of vulnerable people. The makers of a film about a plot to kill Adolf Hitler were barred from filming at military sites in Germany this year because Tom Cruise, its star, is a confirmed Scientologist.
The German defence ministry said the producers "will not be allowed to film at German military sites if Count Stauffenberg - the leader of the unsuccessful plot - is played by Tom Cruise, who has publicly professed to being a member of the Scientology cult".
In July, a Russian court ordered a centre operated by the Scientology movement in St Petersburg to be shut down amid claims of unlicensed teaching and other activities.
But European countries have been criticised by the United States' State Department for labelling Scientology a cult or sect and enacting laws to restrict its operations.
In a statement, Scientology's Europe office said it would contest the proposed charges at the Belgian court hearing.
It said: "For the last ten years, the prosecutor has been using the media, trying to damage the reputation of the Church of Scientology and not being able to put a case in court. As a consequence, this created a climate of intolerance and discrimination [in Belgium]."
The church said the prosecutor's recommendations suggested Scientology was guilty even before a court could hear the charges, making it "difficult" to recover and properly defend itself.
WHO THEY ARE AND WHAT THEY BELIEVE
• THE Church of Scientology was founded in 1953 by the science-fiction writer L Ron Hubbard.
• Scientology is a body of beliefs and related techniques composed of 15 basic books, 15,000 pages of technical writing and more than 3,000 lectures. All its texts are said to have been written by Hubbard, who died in 1986.
• Scientology describes itself as "the study and handling of the spirit in relationship to itself, others and all of life".
• According to the church, the ultimate goal is to get the individual being (the "I", called Thetan) back to its native state of total freedom, thus gaining control over matter, energy, space, time, thoughts, form and life. This freed state is called Operating Thetan.
• Believers in Scientology say that it offers "exact" methods of spiritual counselling to help people achieve awareness of their spiritual existence. The exact nature of all of existence is said to be stated in Hubbard's Scientology and Dianetics Axioms.
• Some central tenets of Scientology are that a person is an immortal spiritual being who has a mind and a body.
• The Thetan has lived through many past lives and will continue to live beyond the death of the body.
• Through the Scientology process of "auditing", people can free themselves of specific traumatic incidents and prior transgressions, which restrict the person from reaching the state of "Clear", and after that, the state of "Operating Thetan".
• Members believe psychiatry and psychology are destructive and abusive.
• Scientology keeps its texts secret until devotees have paid enough money to learn what they say.
• Some opponents claim the cost of completing all the courses can set an individual back $380,000.
• The church itself says the most expensive course it offers is the "Premier Auditor Training Saint Hill Special Briefing Course Package" at $33,932.