The court case arose after charitable and parish organisations in North Rhine-Westphalia complained about strike action launched in 2009 by, among others, the service-sector trade union Verdi.
Employees of Churches and other religious institutions such as charities are governed by their own labour laws in Germany - and have a wide degree of autonomy in terms of pay and working conditions.
Unions wanted to compel religious bodies to adopt regular labour agreements.
In a ruling welcomed by both Verdi and the German Bishops' Conference - each of which interpreted it as a victory - the federal court in Erfurt said labour laws governing the Churches and religious bodies remained valid.
And it confirmed religious employers' right to opt for a joint commission of Church and staff representatives to agree on working conditions which cannot be contested later.
But it also insisted that trade unions must be represented on these commissions and that if this was not the case, the right to strike would apply.