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Erdogan had condemned escalating human rights violations against the Rohingya minority during the phone call earlier in the day, Turkish presidential sources said.
"After the president's conversation with his Myanmar counterpart... Permission was given for 1,000 tonnes of aid to be sent initially," Erdogan spokesman Ibrahim Kalin said in a statement.
The United Nations said 123,600 Rohingya had crossed into neighbouring Bangladesh in the past 11 days following a spike in fighting between militants and Myanmar's military in strife-torn western Rakhine state, which raised fears of a humanitarian disaster.
The latest violence, which began last October when a small Rohingya militant group ambushed border posts, is the worst Rakhine has witnessed in years, with Erdogan last week accusing Myanmar of "genocide" against the Rohingya Muslim minority.
Unverifiable testimony from those who have fled Myanmar has alleged tit-for-tat mass killings and villages being torched by the army, Buddhist mobs and Rohingya militants.
The Rohingya are reviled in Myanmar, where the roughly one million-strong community are accused of being illegal immigrants from Bangladesh.
Kalin said Turkey's international aid body known as the Turkish Cooperation and Coordination Agency (TIKA) would provide rice, dried fish and clothing working with the Rakhine administration, as well as medicine and health products..
The spokesman said TIKA would be the first foreign aid agency to access the region since the violence began.
"At the first stage, 100,000 (Rohingya) families on both sides of the (Myanmar-Bangladesh) border will receive aid," Kalin said, adding military helicopters would be used because of concerns over safety.
Erdogan has stepped up diplomacy and spoken on the phone with Muslim leaders and UN Secretary-General Antonio Guterres seeking ways to solve the humanitarian crisis in Myanmar.
In his phone call with Suu Kyi, a former political prisoner of Myanmar's junta, Erdogan said growing human rights violations against the Rohingya "deeply concerned" the entire world, sources from his office said.
Suu Kyi has come under fire over her perceived unwillingness to speak out against the treatment of the Rohingya or chastise the military.
Erdogan said Turkey "condemns terror and operations against innocent civilians", adding that the developments in Myanmar had turned into a "serious humanitarian crisis which caused worry and resentment.
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