The new programmes, a partnership between the UAE and Malaysia, are aimed at developing scientific knowledge, supporting policy-making, strengthening co-operation and empowering women and girls.
The Sheikh Zayed Chair will be held at the Institute of Strategic and International Studies Malaysia, a leading regional think tank focusing on foreign policy, security studies, economics and social policy.
The programme aims to bridge the gap in study and research about the regions of West Asia and South-East Asia.
It will serve as a research body that contributes to developing policies and providing scientific recommendations to authorities, decision-makers, civil organisations and the youth in the two regions.
The Sheikha Fatima bint Mubarak Chair, named after Sheikha Fatima, Mother of the Nation, will be housed at the National Defence University of Malaysia, the country's first university supporting the development of the armed forces.
The academic programme will be focused on further empowering women and girls in the fields of peace and security, as well as peacekeeping missions at the UN.
It will also aim to strengthen the existing partnership between the UAE and Malaysia.
The announcement comes a day after Sheikh Khaled bin Mohamed held talks with Malaysian Prime Minister Anwar Ibrahim in Kuala Lumpur on Monday.
The two leaders agreed to launch the Sheikh Zayed Chair at the Institute of Strategic and International Studies Malaysia.
They also discussed ways to strengthen ties between the nations in key sectors, including health care, sustainability and transport, as well as strengthening the economic partnership between the UAE and Malaysia.
Sheikh Khaled arrived in the Malaysian capital on Sunday for the start of an official visit, his first since being appointed to the role in March.
Mr Ibrahim was named prime minister in November by the King of Malaysia, Sultan Abdullah Ahmad Shah, after elections produced an unprecedented hung parliament.
The UAE has strong relations with the South-East Asian country that date back several decades.
The Malaysian embassy was opened in Abu Dhabi in 1983, and the UAE embassy in Kuala Lumpur in 1995.