Daglo, whose forces have been at war with the regular army led by Abdel Fattah al-Burhan since April last year, has been touring African capitals on his first visit abroad of the conflict.
He already visited Uganda, Ethiopia and Djibouti as well as Kenya and is currently in South Africa, to the anger of Burhan, whose administration has lost ground to the paramilitaries in recent months and is eager to deny them international legitimacy.
In a statement reported by the official SUNA news agency, Sudan's acting foreign minister Ali al-Sadiq said the ambassador had been recalled "for consultations in protest of the official reception organized by the Kenyan government for the leader of the rebel militia."
He said those consultations would "cover all possibilities for the outcome of Sudan's relations with Kenya."
Ties between Burhan and the Kenyan government have been strained for months, as Nairobi has sought to keep lines of communication open with Daglo so it can mediate in the conflict.
In a New Year’s Day address, the army chief warned that African governments hosting visits by "these killers" were "making themselves a partner in the murder of the Sudanese people."
The war has killed more than 12,190 people, according to a conservative estimate from the Armed Conflict Location and Event Data Project, and forced more than seven million to flee their homes, according to UN figures.
Mediation efforts are largely at a standstill amid deep animosity between the rival generals.
Although Burhan's administration continues to put out statements as the Sudanese government, Daglo's Rapid Support Forces control the streets of Khartoum as well as nearly all of Darfur and much of the central state of Al-Jazira, Sudan's pre-war breadbasket.
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