"It is a serious constitutional issue," the top court said, asking the centre and the Kendriya Vidyalayas to respond within two weeks to a petition that says the prayer is unconstitutional as it promotes a particular religion.
The prayer in Hindi has featured in the morning assembly in more than 1,100 Kendriya Vidyalayas in the country since 1964. There are also Sanskrit words in it.
The court has acted on a petition by a lawyer who argues that the prayer, which the students have to sing with their eyes closed and folded hands, is in violation of the constitution.
"The prayer is in Hindi and Sanskrit. Students of other religions have to compulsorily attend the assembly and recite it," said Veenayak Shah, whose children also studied in the Kendriya Vidyalaya.
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"There is no scientific reason to call this prayer beneficial, so it should be scrapped," said the lawyer.The prayer is "constitutionally impermissible", says the petition, adding that institutions funded by the state cannot propagate any religion.