Dahir Riyale Kahin, president of the unrecognised republic, said the two suspects were detained overnight in the capital, Hargeisa, adding that two other suspects were on the run.
The suspects were part of a group of nine Somaliland natives who received "terrorist" training in camps in and around Somalia's capital, Mogadishu, Kahin said.
Four suspects were captured late on Thursday after a shootout. A fifth suspect was arrested on Friday 30km west of the city.
Three police officers and one suspect were wounded in the clashes.
On Friday, police chief Mohamed Ige Ilmi said the suspects were trained in Afghanistan and possessed assault rifles, anti-tank mines and a large cache of ammunition.
Kahin, however, did not mention links with Afghanistan during a news conference on Saturday.
The authorities were monitoring the suspects as they moved into the region from southern Somalia and the Somali capital of Mogadishu for some time before the intelligence department called for a raid, Ilmi said.
Somaliland has not gained
recognition as a country
They are accused of planning to kill senior government officials and some prominent foreigners in an effort to destabilise Somaliland in the run-up to parliamentary elections scheduled for next week, Interior Minister Ismail
Adan Osman said on Somaliland's official website.
Residents of Somaliland should brace for possible attacks, Kahin said.
European group raised alarm
In July, a Brussels-based group that tracks conflicts around the world said a new group with links to al-Qaida had a foothold in Somalia's capital.
The former British Somaliland and the former Italian Somaliland merged in 1960 to form the independent republic of Somalia.
Somaliland set up its own administration after breaking away from the rest of Somalia because of what they say were clan-based fighting following the 1991 ouster of President Mohammed Siad Barre.
The region has its own security and police forces, justice system and currency but has not succeeded in gaining international recognition.