Tens of thousands of Palestinian refugees in Israeli-occupied East Jerusalem were set to lose education, healthcare and other services provided by U.N. agency UNRWA as an Israeli ban on the organisation takes effect on Thursday.

On Thursday, laws passed by Israel in October come into effect banning the UN’s Palestinian refugee agency, known as UNRWA, from Israeli territory and prohibiting Israeli officials from any contact with the agency.

The United Nation's Palestinian refugee agency said on Sunday it had been ordered by Israel to vacate premises and cease all of its operations in occupied East Jerusalem by Thursday.

The directive came in a letter to the U.N., after the Israeli Parliament banned the relief agency that has aided Palestinian refugees for decades.

Implementation of a ban on the U.N. Palestinian relief agency UNRWA in Israel - due to start on Thursday - will be disastrous, the UNRWA chief told the Security Council on Tuesday, as the United States accused it of being "irresponsible and dangerous.

Israel’s parliament passed two laws last year that will cripple the aid agency's ability to aid Palestinians in Gaza, the West Bank and East Jerusalem