The state education ministry has instructed its secondary teachers to tell pupils about the sect's methods of recruitment and its hidden agenda of psychological manipulation of its members.
The sect is also under scrutiny by the German federal authorities, after suspicions that its activities may undermine Germany's "democratic order". If this were the case the sect could be banned.
At a meeting of Germany's 16 state premiers in Berlin earlier this month there was overwhelming support for the introduction of tough measures to deal with what the Schleswig Holstein premier Heide Simonis described as "this plague of Scientology". They include advice centres to counsel those affected and the declaration of future Scientology offices as businesses rather than religious advice bureaux.
The Church of Scientology was founded by the American science fiction author L Ron Hubbard in 1954. Young people are considered the most at risk of coming under its influence. They are often disillusioned with their lives and seeking a sense of belonging and understanding which Scientologists specialise in providing.
They entice people to become followers through promises of self-fulfilment through the sect's collective good but - critics say - it is often at great financial expense to the convert. These methods will be spelled out in Bavarian classrooms under the theme "new religious movements", which is already a component of RE classes in the overwhelmingly Catholic region.
Claudia Nolte, the federal minister for youth and family affairs, has promised she will combat Scientology with all the powers at her disposal.
Globally, the sect is said to have seven million followers. It has been operating in Germany since 1970. However its claim of 30,000 believers is dismissed by sect experts who estimate the true number to be far lower. None the less Germany is a key link in the group's global chain with an estimated one third of all funds being raised there and in Switzerland.
In Bavaria, the religious-style influence of Scientologists strikes a particularly raw nerve. The education ministry has for some time warned its schools to caution pupils against taking part in street festivals which in reality are undercover recruiting drives.
Anti-sect sentiments may also be somewhat higher in this southern-most state because of its closeness to Switzerland where a bizarre mass suicide-murder by the Order of the Solar Temple occurred last year.
In late January a Dusseldorf court banned a local real estate company from taking on young trainees because it used the same personality test employed by the Scientology movement. The court concluded the tests were used harshly to interrogate young applicants about their private lives and, as such, violated laws on vocational training.