The Turkish Deputy Prime Minister, Bulent Arinc, accused the force of unnecessary delay by alerting them only three days later.
However, the Metropolitan Police said it began working with Turkish authorities a day after the girls went missing and as soon as they had established the facts.
Shamima Begum and Amira Abase, both 15, and Kadiza Sultana, 16, travelled to Istanbul on February 17.
Arinc said: "It is a condemnable act for Britain to let three girls... Come to Istanbul and then let us know three days later.
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"They haven't taken the necessary measures. The search is ongoing.
"It would be great if we can find them. But if we can't, it is not us who will be responsible, but the British."
His comments came after UK police officers travelled to Turkey, although their role in the country has not been confirmed.
A Scotland Yard statement said: "Once we established that the girls had travelled to Turkey, police made contact with the foreign liaison officer at the Turkish Embassy in London on Wednesday, 18 February.
House of Commons' Home Affairs Committee chairman Keith Vaz said there needed to be "much closer cooperation" with Turkey in tackling the problem of people travelling through the country to Syria and Iraq.
British Prime Minister David Cameron has also urged airlines and internet companies to do more to prevent radicalised British teenagers travelling to the Middle East.
The three girls had been studying for their GCSEs, equivalent of Class 10, at Bethnal Green Academy in Tower Hamlets area of east London.
The school's headteacher has said that support was being offered to students and staff in the wake of the incident as students returned to the school after half-term holidays on Monday.
Mark Keary also stressed that there was no evidence that the "radicalisation" of the missing students took place at the school.
The girls' families, who have described them as bright "Straight A" students, have also issued moving public pleas for them to return home.