Tensions between the two sides have soared since early May when drone strikes hit several positions across Port Sudan, the seat of the army-led government, for the first time in the conflict.
Khartoum accused Abu Dhabi of supplying weapons used by its rival paramilitary Rapid Support Forces (RSF), with whom it has been at war since April 2023, to strike its wartime capital.
In a statement, the foreign ministry said Emirati authorities had "deported in the past few days most of its personnel at the Sudanese general consulate in Dubai without (providing) any reasons".
It added that the diplomats "were detained for eight hours" at Dubai airport after completing their departure procedures.
During that time, the ministry said, they were interrogated and had their phones and laptops searched in what Khartoum described as "grave and blatant violation" of international diplomatic conventions.
"This unprecedented incident reflects a grave disregard by the Emirati authorities for their obligations under international law, which requires them to protect diplomats and grant them the necessary immunities and privileges," the statement read.
"This action also reflects a desire to harm Sudanese nationals residing in the UAE," it added.
The UAE's foreign ministry was not immediately available for comment.
Abu Dhabi has long denied supporting the RSF, despite reports from UN experts, US politicians and international organisations.
Early this month, drone strikes pounded key infrastructure in Port Sudan, including its only functioning international civilian airport, a major fuel depot and the main power station.
The army pointed fingers at the RSF, calling them a "proxy" of the UAE.
The conflict in Sudan, now its third year, has killed tens of thousands, displaced 13 million and created the world's worst humanitarian crisis.
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