Initially TKM Centenary School in Kollam, 65km south of Thiruvananthpuram, had planned a dance fusion with Vande Mataram playing in the background. But it was replaced with an orchestra after workers of the Social Democratic Party of India (SDPI) threatened to disrupt the programme.
The national song was dropped after several rounds of rehearsals.
When the issue snowballed into a raging controversy, school management denied any external pressure.
Various student outfits later took out protest marches to the school seeking strict action against the management and the principal.
However, the SDPI justified the changes in the programme.
"We approached the school management after a number of parents complained that some words in Vande Matraam and the gesture namaste were against their religious belief. We only requested the school to respect their sentiment," said SDPI leader AK Salahuddin.
Police said they received a complaint and started an investigation in this regard.
School principal Latha Alexander was unavailable for comments.