Mrs Adefisayo said the government "promotes and runs a public school system devoid of politics and political insinuations".
The Lagos State Government said it has commenced an investigation following the report from a parent that her 10-year-old daughter was sent out of Odomola Junior Secondary School, Epe, over an election campaign poster.
The mother had claimed in a viral broadcast message that her daughter, Marvelous Barinaadaa, was sent out for using the poster of the Labour Party presidential candidate, Peter Obi, to wrap her notebooks.
However, in a statement signed by the Assistant Director of Public Affairs, Lagos State Ministry of Education, Ganiu Lawal, on Thursday, the government noted that "all its agencies will never instruct any school principal, personnel or teacher to act in such a manner."
It noted that the Commissioner for Education, Folasade Adefisayo, has reassured that the matter will be dealt with "within the scope of our strict regulations as the reason for sending home the student is unacceptable - if true."
"Student found selling election posters"
The Epe Coordinator of Child Protection Network (CPN), Togun Olusegun, confirmed that the organisation is on the issue. He said his organsiation already spoke with the school authorities and would visit the school on Friday for further findings.
According to Mr Olusegun, "the student was not suspended but was asked to leave the school when she was caught selling the election poster for N50 within the school premises."
Mr Olusegun explained that the principal made the decision to avoid crisis, noting that political activities are not permitted in the school.
In the viral message, the mother of the student accused the school of sending her daughter home without informing the parents. She referenced a short letter signed by the school principal, which reportedly reads that: "the student is permitted to go home to campaign for Peter Obi against the will of Lagosians."
"This girl is just ten years old, she didn't know anything about politics, but she was sent away from school without informing the parent because they say we support Peter Obi and Labour Party," the mother said.
"Please, is this act by the school principal good? See what the school Principal wrote in that letter? And after we say we are one Nigerian," she said.
Lagos to discipline defaulters
Meanwhile, in the statement by the government, the commissioner hinted that another school principal at Odonguyan who was caught on camera promoting her political choice to the students has been subjected to appropriate disciplinary measures.
Mrs Adefisayo reiterated that the Lagos State Ministry of Education "promotes and runs a public school system devoid of politics and political insinuations".
"A thorough investigation of the matter will be carried out and anyone found culpable will be subjected to disciplinary measures as laid down in the civil service rules," she added.