In a radio broadcast on Sunday, Gedi also urged government members to leave the Somali capital and join him in the southern town of Jowhar, where he has temporarily set up operations because Mogadishu is considered unsafe.
On Friday, Somalia's president and parliamentary speaker ended talks in Yemen without resolving differences that have split the transitional government as it struggles to set up operations after returning home from exile.
President Abdullahi Yusuf Ahmed and parliament Speaker Sharif Hassan Sheikh Aden failed to agree on where the government should be based and on the involvement of troops from neighbouring countries in a regional force that would be sent to stabilise the country.
The president wants government to set up in Jowhar, about 60 miles northwest of the capital. The speaker, however, insists they be in the capital, as provided in the transitional constitution.
The speaker has set up operations in Mogadishu, together with more than 100 legislators who are pressing the president, prime minister and the rest of the cabinet and parliament to follow suit.
"There is no division within the government, but few individuals are trying to sabotage the Somali peace process," Gedi said during the radio address marking the independence of the Somalia's northern regions from British colonial rule.
Government figures are divided
on foreign troop deployment
"We urge them to join the majority of members of the government - if not, we will confront them by force with the support of Somali people."
The president and speaker also failed to agree on the presence of troops from neighbouring countries, including Ethiopia, in a regional force that would be sent to secure the government and key installations, help disarm thousands of militia fighters and train security forces.
State of chaos
The president supports troops from neighbouring countries. Powerful leaders turned cabinet ministers who control Mogadishu and other legislators disagree.
Somalia has not had an effective central government since clan-based leaders overthrew ruler Mohamed Siad Barre in 1991. The leaders then turned on each other, plunging the country of seven million into chaos.
The transitional government has been based in the Kenyan capital Nairobi since it was set up last year because Mogadishu is too insecure.
Gedi, lawmakers and members of his cabinet returned home On 18 June, setting up operations in Jowhar. The president, though, has yet to return home.