The council said criticisms of its handling of the case of Shamima Begum - whose British citizenship was revoked by the government earlier this year - were "unfair and skewed" and it had some of the "strongest measures" in place to prevent radicalisation.
The comments came as the now 19-year-old's lawyer, Tasnime Akunjee, said he had written to the Home Secretary accusing both the council and the police of failing to protect the Bethnal Green schoolgirl from being radicalised.
In a letter, seen by the BBC, Akunjee said the teenager's family was not told she had been interviewed by police when another girl at the same school left for Syria some months earlier.
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Akunjee said that by questioning the girls without their parents, they were put on notice that "they were being monitored and would have to leave for Syria immediately" and had the family known they might have able to stop their daughter from travelling.
Begum left the UK in 2015 with two other pupils at Bethnal Green Academy, 15-year-old Amira Abase and 16-year-old Kadiza Sultana.
In February, Begum was found in a Syrian refugee camp pregnant with her third child and said she wanted to return back to the UK. The baby died three weeks after being born.
Home Secretary Sajid Javid refused her entry back into the UK and she has since been granted legal aid to fight the decision to revoke her British citizenship.
Akunjee described the chain of events leading up to her departure in 2015 as "arguably the worst case of child radicalisation in the western hemisphere" and criticises Tower Hamlets for not launching a serious case review.
He said it was only after Begum left the UK with her two friends that the council made the four remaining girls wards of court to protect them from being radicalised.
Tower Hamlets said a "multi-agency partnership gold group" including the police and health services found Begum's case did not meet the threshold for a serious case review.
The teenagers had not been known to social services before she left for Syria as the police, her school, the NHS and other bodies had not raised any concerns about her welfare, it added.
"Instead the council worked alongside the government's Prevent team and the police's SO15 counter terrorism team to provide in-depth support to the school, its staff, parents and pupils in order to investigate what had happened and stop others following in their footsteps," a statement issued by the council said.
The council's mayor John Biggs said the allegations made by the family's lawyer were not a "fair reflection" of the situation.
"We have put in place robust measures to help prevent radicalisation in our schools, including intensive work with their school.
"In Tower Hamlets we pull together and tackle extremism in all its forms. Shamima Begum will have to account for her actions and we will see what happens next which is a matter for the government," he said.
An Ofsted inspection of the council in 2017 praised its work to help prevent radicalisation for having "extensive knowledge" and providing "creative and sensitive work to engage families through strategy discussions and child protection investigations to help protect children from violent extremism".
A Home Office Prevent peer review in 2018 found the council to have an "extremely strong approach to Prevent" with "strong leadership from the mayor and chief executive", the statement added.
A spokesperson for the Home Office said it would not comment on individual cases.