Mr Roble announced that Internal Security Minister Hassan Hundubey resigned and his position had been filled.
However, President Farmaajo later announced that the prime minister has no powers to make such a decision.
Somalia’s President Mohamed Farmaajo has overturned yet another major decision made by Prime Minister Hussein Roble as differences between the two leaders escalate.
This comes after Mr Roble announced that Internal Security Minister Hassan Hundubey resigned and his position had been filled.
On Wednesday, Mr Roble appointed Abdullahi Mohamed Nur, a member of the outgoing parliament, to replace Hundubey.
However, President Farmaajo later announced that the prime minister has no powers to make such a decision.
“Based on Article 90, point (e) of the Provisional Constitution, the powers of the president include ‘the firing of the ministers, state ministers and the deputy ministers upon proposal from the prime minister,’” Farmaajo’s statement said.
“No appointment or dismissals of the cabinet members are workable until all constitutional means are exhausted.”
The president said Mr Roble’s current job is to deal with the election implementation and other state priorities.
There has been debate on whether Farmaajo’s administration is a caretaker government given that its term elapsed and Somalia is due to hold delayed elections.
In additional, transitional clauses in the Provisional Constitution give the Prime Minister overall control over the government, especially the Council of Ministers.
But Somalia’s lack of strong courts to help interpret the law has led to political leaders interpreting it as they wish.
Mr Yasin has been in the eye of storm after 25-year-old intelligence agent Ikran Tahlil Farah disappeared in June, and the National Intelligence and Security Agency (NISA) last week declared that the spy had been abducted and killed by Al-Shabaab militants. The militants denied the accusations.
Ms Tahlil’s family has also rejected NISA's explanation.
PM Roble suspended Mr Yasin at the weekend to pave way for investigations. Hours later, President Farmaajo cancelled the suspension. Later, his office announced that Mr Yasin had resigned from the position of spy chief and been appointed senior national security advisor.
Farmaajo then appointed Yasin Abdullahi Mohamud to replace Mr Yasin at NISA in an acting capacity.
However, this left questions on what role Bashir Mohamed Jama would play, as PM Roble had appointed him to lead NISA when Mr Yasin was suspended.
Mid-morning Wednesday, NISA’s official Twitter account indicated that Farmaajo’s appointee had taken over office.
