The minister, Numan Kurtulmus, warned that Turkey was facing "a refugee wave that can be expressed by hundreds of thousands."
"This is not a natural disaster...What we are faced with is a man-made disaster," Kurtulmus said of the surge of mostly women, children and the elderly that started late Thursday.
The situation has raised tensions between Turkish authorities and Kurds, who claim the government is hampering their efforts to help their brethren in Syria by refusing to let Turkish Kurds cross into Syria.
The conflict in Syria had already pushed more than a million people over the border since it began in March 2011. Refugees yesterday reported atrocities by Islamic fighters that included stonings, beheadings and the torching of homes.
"We don't know how many more villages may be raided, how many more people may be forced to seek refuge," Kurtulmus said. "An uncontrollable force at the other side of the border is attacking civilians."
The al-Qaida breakaway group, which says it has established an Islamic state, or caliphate, ruled by a harsh version of Islamic law in territory it captured straddling the Syria-Iraq border, has recently advanced into the Kurdish regions of Syria that border Turkey.
Turkey had previously been reluctant to take part in international efforts against the group, citing the safety of 49 citizens taken hostage in June when the Islamic group overran the Iraqi city of Mosul.
But on Saturday, Turkey secured the hostages' release but would not say how. President Recep Tayyip Erdogan has denied paying a ransom but has been vague on whether there was a prisoner swap.
Fighting raged today between Kurdish fighters and the militants near the northern Syrian city of Kobani, the Britain-based Syrian Observatory for Human Rights said.
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