Hundreds of students shouted slogans and carried placards critical of India's ties with the Jewish state while Mukherjee was being honoured by Al-Quds university at Abu Dis with an honorary degree and hailed as a "Knight of Peace".
After the university function, Mukherjee was to inaugurate a secondary school for boys named after Jawaharlal Nehru. But the function was called off due to the tense situation.
Mukherjee soon left for Israel, a short journey by road, on the first-ever visit by an Indian President.
The demonstration came in the middle of heightened tensions and more killings between Israelis and Palestinians which have resulted in hundreds of casualties, including some today.
Inside the university auditorium, where Palestine Prime Minister Dr Rami Hamadallah Mukherjee was among those present, Mukhkerjee was hailed as "a Knight of Peace" and loudly cheered when he mentioned all the help rendered by India to the Palestinians.
Mukherjee, who is in Palestine in the first-ever State visit by an Indian President, also announced an increase in Indian Technical and Economic Cooperation(ITEC) scholarship programme slots for Palestine to 100 per annum and setting up of an India-Chair at the Al-Quds University.
On Sunday, the President was conferred with an honorary degree in political science by the University of Jordan in Amman. On Thursday, he will be conferred a honorary doctorate by the Hebrew University in Israel.
"India will build a similar Center in Gaza. We look forward to the success of the Techno-Park in Ramallah. It will be jointly built and operated by the Palestine Investment Fund and the Indian public and private sector," he added.
