Mr Qandil said Saturday's incident "sheds light on the nature of people occupying the square".
BBC: Tahrir Square activists confront Egypt PM Hisham Qandil
In recent days, the Turkish military bombed suspected PKK camps in the Qandil Mountains of northern Iraq.
CNN: Mourners in Turkey protest killings of Kurdish activists
Egyptian Prime Minister Hisham Qandil says he was confronted by "youths and troublemakers" on Cairo's Tahrir Square amid continuing opposition unrest.
BBC: Tahrir Square activists confront Egypt PM Hisham Qandil
The organisation still has several thousand fighters, many of whom are based in the Qandil mountains of the Kurdish region of northern Iraq.
In Egypt, Hisham Qandil, whom President Muhammad Morsi has appointed as prime minister, announced a cabinet composed largely of technocrats with a handful of Islamists.
Turkish warplanes routinely strike bases of the Kurdistan Workers' Party, or PKK, a Turkish rebel group operating from the Qandil mountains of Iraq's Kurdish region.
In a statement Mr Qandil said he had been "accosted" by protesters on Tahrir Square on Saturday, adding that he "preferred to avoid a confrontation between them and security personnel".
BBC: Tahrir Square activists confront Egypt PM Hisham Qandil
Mr Qandil will hold a meeting with members of his government on Saturday to discuss the next steps on seeking an International Monetary Fund (IMF) loan, he said, according to the Reuters news agency.
Its prime minister, Hisham Qandil, told Mr Haniyeh to conciliate his Palestinian rivals under Mahmoud Abbas who run the Palestinian Authority based in Ramallah on the West Bank, if he wanted relations with Egypt to improve.
"We hope that there will not be any fundamental changes in our plan with the IMF because we will summon them in January so we resume discussions to go forward in the matter of the loan, " Mr Qandil said.
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