During a meeting at the AU headquarters in Addis Ababa on Sunday with Somali Prime Minister Hassan Ali Khaire, Faki said such actions threaten peace-building efforts in Somalia, according to a statement from the AU.
Without referring to specific countries, Faki urged all "concerned external actors" to "refrain from any actions that might undermine Somalia's progress", saying such action "risks reversing the hard-won gains so far made in the country thanks to the sacrifices of African Union Mission in Somalia [AMISOM] forces and the Somali security forces".
Faki acknowledged the progress made by the Federal Government of Somalia, particularly the adoption of a Transition Plan, which provides for a gradual handover of security responsibility from AMISOM to the Somali Security Forces.
Similar concerns were raised in a two-day seminar by EU envoys in East Africa on Saturday, who voiced concern over the repercussions of Gulf crisis on Somalia.
The ongoing GCC crisis began almost a year ago when Saudi Arabia, the United Arab Emirates (UAE), Egypt and Bahrain cut diplomatic ties with Qatar over Doha's alleged support for "terrorism", allegations Qatar vehemently denies.
Alexander Rondos, Europe's special envoy to the region, said the fallout has had direct repercussions in the Horn of Africa where it has exacerbated already existing tensions, notably in Somalia.
Tensions have escalated steadily between Somalia and the UAE, which has sought to extend its influence there.
Although the two countries have been traditionally close, Mogadishu's attempts to remain neutral over the Gulf divisions have not gone down well.
In April this year, the UAE ended support for both a military training programme and a hospital, which it ran in the Somali capital, Mogadishu.
Rondos said one of the EU's "most important objectives" is to make sure that East Africa "is as well protected as it can be from what is a rapidly shifting geopolitical environment" in the Gulf.