"Turkey cannot stand by as Kurdish, Leftist and Islamic State militants target Turkey," said Mr Davutoglu. "We will take necessary measures against whoever constitutes a threat to our border."
The Isis members arrested were part of the extremist group's higher management in Turkey, said Sinan Ulgen, head of the Turkish think tank Edam in Istanbul. He called the strikes a "turning point" but feared reprisals by Isis.
On Monday, an Isis-linked suicide attack on a mainly Kurdish youth group in the border town of Suruc killed 32 people and injured more than 100. Two days later, the paramilitary wing of the Leftist Kurdish Workers Party retaliated, executing two soldiers in their homes for alleged complicity with Isis.
Ankara's new deal with the White House will allow US forces to launch warplanes and Predator drones, some equipped with Hellfire missiles, from airbases at Incirlik and Diyarbakir, close to the border with Syria. The Turkish military said it would also take part in the operations.
Erdogan's Government has been criticised for its apparent tolerance of Isis, which has used Turkey's southern border as a transit hub for foreign fighters and goods.
Many have accused Ankara of supporting Isis in its bid to overthrow Bashar al-Assad's regime in Syria.
The week's unrest has knocked Turkey's already flagging economy, causing the Turkish lira fell to 0.36 against the US dollar.
The Turkish Government has already announced plans for a high-level security barrier along its 800km border with Syria.