The Israeli Ministry of Education described the victory of a Palestinian pupil from East Jerusalem, as a "provocation".
The ministry made the remarks while commenting on a female Palestinian student who came second in a maths competition in Dubai as the "Jerusalem representative from Palestine" despite her school receiving funds from Israel.
Last week, Dar Al-Hekmah, a school located in East Jerusalem which receives 75 per cent of its funding from the Israeli Ministry of Education, sent a female student as its representative at the Arab mathematics competition in Dubai.
After coming second in the completion, the girl was presented as the "Jerusalem representative from Palestine". She even took a picture with the Palestinian flag as she stood on the podium to receive her prize.
A few days later, she returned to her school in East Jerusalem. However, the ceremony in her honour was held at the Palestinian Education Ministry in Ramallah.
Palestinian Education Ministry tweeted: "Congratulations! I congratulate Palestine on the second place win in the world mathematics competition."
The Israeli Education Ministry stated in response: "The Education Ministry views this provocation very seriously and the principal of the school will be summoned for a talk."
This incident brings to light Israel's perception of the occupied territory including East Jerusalem, which under international law is occupied territory but in the eyes of many Israeli politicians it is their "eternal capital city".