Nicky Morgan has written to the school attended by three girls feared to have disappeared to Syria to join Islamic State (Isis) fighters, offering her support, adding that she was sure the school was doing “everything possible” to keep students safe.

In her letter to Mark Keary, the principal of the Bethnal Green Academy in East London, the education secretary said she was aware that it was a “difficult time” for the school, but was confident everything was being done to give students a “safe and tolerant” environment in which to learn.

The letter comes just hours after the Metropolitan Police issued a statement raising fears that the three teenagers, Shamima Begum, 15, Kadiza Sultana, 16 and Amira Abase, 15, have now crossed from Turkey in Syria.

The alarm was raised last week after the three students boarded a plane to Istanbul, Turkey from Gatwick Airport, with the intention of travelling to Isis-controlled parts of Syria.

The girls’ disappearance follows that of another 15-year-old student from Bethnal Green Academy who went missing in December after travelling to Syria via Turkey.

In her letter, Ms Morgan thanks the school’s staff for providing “reassurance to parents and pupils on their return to the school” this week after the half-term break.

“I know this must be a difficult time for everyone involved with Bethnal Green Academy, but I understand from my conversations with the regional schools commissioner Tim Coulson that your communication with parents and pupils has been clear and effective, and that you feel confident that everything possible is being done to keep pupils safe,” she says.

“While we hope and pray for the safe return of the pupils in question, we also think of their friends and acquaintances at the school who will no doubt struggle to come to terms with the events of recent days.”

She adds: “I know that you and the staff there are doing everything possible to provide them with the help and support they need and to ensure they continue to thrive in a safe, tolerant environment where the fundamental British values of democracy, the rule of law, individual liberty, mutual respect and tolerance are promoted and widely shared.”

On Monday, Mr Keary issued a statement saying that he was “deeply shocked and saddened” by the news, and added that there was “no evidence” that any radicalisation had taken place at the academy.

It is believed that the girls may have been recruited to join Isis fighters via social media websites, including Twitter and Facebook.

Mr Keary made clear that access to social media networks was “strictly regulated” at the school, and students were unable to access Twitter or Facebook on academy computers.

“With such measures in place, police have advised us that there is no evidence that radicalisation of the missing students took place at the academy,” he said.

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