Prosecutors in the trial of Nurpashi Kulaev had originally intended to hear testimony from 69 witnesses.
The court decision came two days after the Beslan Mothers pressure group lodged a complaint that the prosecution was excluding witnesses who victims' relatives believe could give the most objective testimony.
The Beslan Mothers group has accused prosecutors of seeking to divert possible blame for the siege's high death toll from federal security troops.
Over 330 people were killed in the September 2004 Beslan massacre. More than half the victims were children.