Arfa Iftikhar was forced into hiding after a furious mob stormed Farooqi Girls' High School in the eastern city of Lahore over a piece of homework she set that allegedly contained derogatory references to the Muslim prophet Mohammad.
Blasphemy is an extremely sensitive issue in Pakistan, where 97 per cent of the population are Muslims, and allegations of insulting Islam or the prophet Mohammed can prompt violent outbursts of public anger, even when unproven.
The school management took out front page adverts in two leading newspapers on Friday to deny it had any knowledge of the supposed insults to the prophet, saying Iftikhar distributed the work just 10 minutes before the school closed for the Eid al-Adha holiday.
"Our school management and the owners have no link whatsoever with this dirty act," the advertisement in Urdu said.
"We appeal to the government and the police to take legal action against this teacher and investigate her real motive".
The school's headmaster Asim Farooqi has been remanded in custody for 14 days on charges of blasphemy, which can attract the death penalty, police officer Azam Manhais said, while a search was under way for Iftikhar.
Mr Farooqi's lawyer Jawad Ashraf said they would apply for bail on Saturday and accused police of bowing to the mob over the headmaster's arrest.
"It seems his arrest was made on public pressure but we see that he has no role in this entire case except some negligence as principal of this school," he said.
Activists say Pakistan's harsh blasphemy laws are often abused to settle personal scores, and Mr Ashraf said the possibility of a conspiracy against the school, one of the most successful in Lahore, could not be ruled out.
Mr Farooqi's son Sameer Asim Farooqi, one of the school's administrators, said the way the case had panned out was "strange".
"It seems that an organised gang attacked our school. The attackers were mostly teenagers and they had batons in their hands, but some of them were also armed (with firearms)," he said.
"We also heard there were announcements in the nearby mosques about the incident to inflame the public."
Sameer Farooqi said Iftikhar had been sacked, despite telling the principal she had copied out the offending passage by mistake.