A video of several male students at Oldham Academy North praying outside has been widely shared on social media sites, with people claiming the group were forced to move out of the building and into the cold.
The video has been met with widespread anger, with many calling the incident "disgusting".
The school have since said students were not able to use a room inside as a flood had closed 15 classrooms at the school.
A joint statement from Oldham Academy North, Oldham Council, and the Oldham Interfaith Forum read: "Earlier this week photos on social media began to circulate of students at The Oldham Academy North praying outside.
"The Oldham Academy North, Oldham Interfaith Forum and Oldham Council would like to address the understandable concern this has caused.
"Firstly, the academy would like to offer a wholehearted apology.
"The school is proud of its diversity and would never stop students from praying or ask them to pray outside.
"This situation arose due to a lack of space in the school, caused by a flood which created a huge amount of damage and made 15 rooms unusable.
"A room has since been found for students to pray in, and we understand they are happy with the space.
"The academy is writing to parents today to fully explain what has happened, and are happy to meet with any members of the community who are concerned."
Oldham Council Leader, Arooj Shah, added: “When we were made aware of the issues raised at the Oldham Academy North, we acted quickly to speak with the school to understand what had happened.
"Having spoken with the school leaders I am glad they have apologised to those who were affected and will be writing to parents to explain.
“Oldham is a proud and diverse borough and I know that the Oldham Academy North sees this as a strength for the school.
"We will continue conversations with the school around this matter to investigate the situation properly.”
Oldham Mosques Council Development Officer, Mufti Helal Mahmood, said: “We will be working closely with Oldham Academy North to ensure incidents like this can be avoided in the future.
"We have a strong history in Oldham of working together across different communities and faiths.
"We must not let ourselves be divided when issues arrive but work through them in partnership to achieve peaceful resolutions.”
Source: Manchester Evening News