Members of the Somali parliament allied to Abdullahi Yusuf Ahmed, the president, have said that they are in hiding after they received death threats.
The group said on Thursday that they were in Baidoa, in south-central Somalia, after militia men and soldiers entered parliament.
Mohammad Adow, Al Jazeera's correspondent in Nairobi, the Kenyan capital, said that the house had split between the president's supporters and those backing Sheikh Adan "Modobe" Mohamed, the speaker of parliament.
Both the president and the speaker claim different individuals as prime minsiter. Yusuf appointed Mohamed Gamodheere as prime minister on Tuesday and Modobe backed Nur Hassan Hussain a day later.
Hussain and Modobe are preparing a motion to impeach Yusuf, who is said to be battling against that occurrence.
Abdikadir Nour Arale, a member of parliament, told Al Jazeera from Baidoa: "What they have seen in parliament was terrifying because a number of soldiers and militia men walked in to parliament to silence those who wanted to express freely what they feel about the way in which the speaker is handling this delicate issue.
"And since then, almost a half of the parliamentarians didn't dare to go to the parliament and stayed in other places for security reasons."
However, Arale said that the members were also staying away because they had a lack of confidence in the speaker and his handling of parliament.
'Beginning of the end'
"Many believe that this is the beginning of the end of the Somali transitional federal government due to the depth of divisions between supporters of the president and the speaker of parliament," Adow said.
"There are now two prime ministers, one with the president and one with the speaker of parliament.
"And both are now planning to appoint cabinet ministers, which would mean Somalia would have two parallel governments."
Adow said that it appeared difficult for the speaker to get the benchmark two-thirds of the 275 member parliament needed to impeach the president.
However, he said that the extent of the split in government meant that the safety of Yusuf's allies in Baidoa could not be guaranteed.
'Situation getting worse'
"The situation is getting worse and Baidoa might not be the best place for the president and his allies.
"Baidoa is a very volatile area ... security would not be very good for those who are opposing the speaker, who hails from that area and is one of the former war lords who have been controlling parts of Baidoa and the Bay region as a whole."
Local reports said on Wednesday that Modobe had claimed to have 117 parliament signatories to impeach Yusuf on allegations of violating the constitution and ruling the country under a system of dictatorship.
The split in the Ethiopian-backed interim government comes as opposition Islamist forces maintain their assault against the state and continue to gain ground across Somalia.
The country has suffered 17 years of civil war, with the latest proposal for a new peacekeeping force gaining little ground with UN members this week.