The mission will operate under the International Renewable Energy Agency (IRENA), of which Israel is a member, foreign ministry spokesman Emmanuel Nahshon told AFP.
Establishing a permanent presence in Abu Dhabi will not change Israel's official relationship with the UAE, which does not recognise Israel and has no diplomatic ties with it.
But as the headquarters for an international organisation, the Emirates is obliged to accept an Israeli representative under United Nations guidelines.
Signup to our newsletter and follow us on Facebook and Twitter!
The UAE foreign ministry stressed in a statement that "any agreement between IRENA and Israel does not represent any change in the position of the UAE or its relations with Israel".
The functions of the missions accredited to IRENA "are limited to their communications and dealings with the agency," ministry spokeswoman Maryam al-Falasi said in a statement carried by WAM state news agency.
"They do not, under any circumstances, cover any other activities and do not involve any obligation upon the host country with regards to its diplomatic relations or any other relations," she added.
The presence of a permanent mission in Abu Dhabi is likely to boost diplomatic efforts by Israeli Prime Minister Benjamin Netanyahu who has repeatedly stressed that a nuclear deal between Iran and world powers opens the door to closer Israeli-Arab ties.
The mission has been the subject of years of top secret discussions, according to the Israeli daily Haaretz.