The boys went with their mother, Shamsa Imam, to Pakistan to attend memorial events of their late father who died because of cancer.
The boys Hussain, and Mustafa, both 12, are at risk of being struck off the school’s register.
School bosses say places cannot be held if anyone if absent for unusual amount of time, and six weeks is unusual.
The mother claims it was essential that they went to Pakistan to meet close family members and attend the burial.
Gorton MP Afzal Khan has written a letter to the school requesting not to kick out the boys.
Shamsa Imam said “We believe that there is a high chance that this will happen,”
“The kids have always been fully up to date with their work and are continuing using a variety of learning materials to keep their learning up to date.”
Angelique Bueler, a family friend also requested the school bosses to take their decision back.
She said: “The kids only had a few days off when it first happened. Shamsa needed to spend time with her family. Her GP advised her to take a trip to Pakistan to be with family. She didn’t have much option but to take the kids because she’s a single parent now and her health is suffering.
“The kids have been really good in school all through their dad’s illness.”
They have started a online petition requesting the bosses of the school to let boys study in the same school.
The academy principal Tarun Kapur sayd children are supposed to be in school unless there are exceptional circumstances.
He said the trust consults and takes advice from the local authority if a child is absent from school for a long period.
“Because of the great demand for places it’s wrong for us to hold places when there are rules to say if a child is away for ‘x’ number of weeks we should think about taking them off roll,” he said.
“In this particular case we have been really empathetic.
“We expect children to be in school unless there are exceptional circumstances. If someone is away for an inordinate amount of time we take advice from the local authority.
“We try to make sure that children are allowed time off in exceptional circumstances but six weeks is unusual.”
According to the department of education, a child can be removed from the school register if he is absent for over 20 days.