Shamima Begum and Amira Abase, both 15, and Kadiza Sultana, 16, travelled to Istanbul a week ago.
The girls boarded a Turkish Airlines flight at Gatwick, and would have required a visa to enter the country.
Deputy Prime Minister Bulent Arinc said officials would have taken "necessary measures" had they had known earlier.
Mr Arinc said: "We have tracked down and banned tentatively 10,000 people who were previously reported to us from entering Turkey on suspicions of terrorist activities. We fulfil our duty.
"We believe that there is a need for joint effort and coordination in fight against terrorism."
His comments came after UK police officers travelled to Turkey, although their role has not been confirmed.
Scotland Yard said: "Officers are working closely with the Turkish authorities who are providing a great deal of assistance and support to our investigation."
Security services have already faced criticism after it emerged that, before leaving the UK, Shamima sent a Twitter message to Aqsa Mahmood, who left Glasgow for Syria in 2013 to marry an Islamic State fighter.
According to a lawyer for Ms Mahmood's family, her Twitter account has been "monitored" by police since she left Britain.
He said authorities should have seen Shamima's message and taken action before she and her two friends followed.
The girls were all studying for their GCSEs at Bethnal Green Academy in east London. Their head teacher Mark Keary said on Monday there was no evidence they had been radicalised at school.
The girls' families have made appeals for them to come home.
