The Government of National Unity has rejected the Presidential Council's (PC) decision to suspend Foreign Minister Najla Al-Manqoush from her position.
In a statement early on Sunday, the GNU hailed Al-Mnqoush's efforts and confirmed she would carry out her duties normally.
On Saturday, a spokeswoman for the PC said that Al-Manqoush was suspended for carrying out foreign policy without coordination with the council.
The GNU's statement said that according to the political dialogue signed in Geneva, the Presidential Council has "no legal right to appoint or cancel the appointment of members of the executive authority, suspend them or investigate them", adding that these powers are exclusive to the prime minister.
It stressed that the consensual basis that has been predetermined by this stage requires coordination between the PC and the GNU to prevent any new political crisis.
In another development, the foreign minister denied Sunday that her comments about the 1988 Lockerbie bombing in a BBC interview had anything to do with extraditing Abu Agila Masoud wanted by the US for links to the incident.
The US alleges that Masoud, a former member of Libya’s intelligence services, assembled and programmed the bomb that blew up Pan Am Flight 103 over the Scottish town of Lockerbie in 1988, killing 270 people.
Talking to the BBC this week, Al-Manqoush said there are "positive outcomes coming" in the Lockerbie case.
In response to a question about any plans of extradition, she said "I don't know, but we as a government are very open in terms of collaboration on this matter.
Her comments were read by some as a "potential extradition" of Abu Agila Masoud to the US.
A statement issued on the Foreign Ministry's Facebook page said that Al-Manqoush was responding to a question about the Lockerbie and the Manchester Arena bombing.
The statement quoted the foreign minister as saying that these issues are within the jurisdiction of the Attorney General's Office, which is responsible for discussing the matter with the judicial institutions in both countries, alerting that circulating such misleading news is one of the crimes punishable by law.