Sheikh Mohamed, the UAE President, met Turkish Defence Minister Hulusi Akar on Monday in Abu Dhabi.
The pair discussed the prospects of further co-operation between the two nations.
Mr Akar conveyed the greetings of Recep Tayyip Erdogan, Turkey's President.
He offered his condolences after the death of Sheikh Khalifa this month and congratulated Sheikh Mohamed on his election as President.
Sheikh Mohamed reciprocated his greetings to Mr Erdogan, Wam news agency reported.
The meeting was attended by Sheikh Mansour bin Zayed, Deputy Prime Minister and Minister of Presidential Affairs; Sheikh Hamdan bin Mohamed; Sheikh Mohammed bin Hamad, adviser for special affairs at the Ministry of Presidential Affairs; Mohammed Al Bowardi, Minister of State for Defence Affairs; Sheikh Shakhboot bin Nahyan, Minister of State; and Lt Gen Hamad Al Rumaithi, Chief of Staff of the Armed Forces.
