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Guterres spoke by phone earlier with President Hery Rajaonarimampianina and they both agreed to immediately send UN special adviser Abdoulaye Bathily.
Two people were killed and at least 16 wounded in protests in Madagascar's capital over the weekend, which the president has denounced as an attempted coup.
Bathily will work closely with the African Union and the Southern African Development Community (SADC), said UN spokesman Stephane Dujarric.