Judge Robert Stack's decision comes after a trial that was supposed to start last week was delayed by procedural arguments.
A lawyer defending the federal government against allegations of abuse and cultural losses raised concerns that third parties weren't ready.
At issue was the extent to which defendants named by Ottawa and the province were to take part in the first of a two-phase trial.
Stack now says all parties are to be ready for a single, 12-week trial to start Sept. 28, 2015.
More than 1,000 Metis, Inuit and Innu plaintiffs want an apology and damages after they were excluded from a federal apology and compensation deal.
Lawyers for the federal government deny it was responsible for five schools that opened before the province joined Confederation in 1949.
The International Grenfell Association ran three of the schools, while the Moravian Missionaries ran the other two.