A woman casts her vote at a polling station in Semonkong, Lesotho on Saturday. (Photo: Themba Hadebe/AP)

Foreign observers on Monday described Lesotho's weekend election as "largely peaceful" despite the shock deployment of armed soldiers at polling stations on voting day.

Counting was under way Monday in the restive mountain kingdom, which has been rocked by attempted coups and instability in recent years.

Regional observers said the snap polls were "largely peaceful" but called for post-election reforms to bring stability to a country hit by chronic political infighting and suffering from weak government institutions.

"Elections alone cannot address the underlying political and structural challenges facing the country," said former Mozambican president Joaquim Chissano, who headed a team of African Union observers. He called for parliamentary and judicial reforms as well as a change in the role of the security forces.

Lesotho's army has often been accused of interfering in politics and its unexpected deployment during the vote caused heavy criticism. The electoral commission said the presence of the military at polling stations had caused confusion.

"The nation, the voters and even the observers were surprised… they felt that some voters were intimidated," Independent Electoral Commission spokesman Tuoe Hantsi told reporters.

The South African Development Community (SADC) regional bloc said the involvement of the army could be "misconstrued as military interference" and could "influence the conduct of the election".

The vote was the third general election since 2012 in the country known as Africa's Switzerland where years of political friction, including a failed coup, have stymied attempts to fight dire poverty. Lesotho has a 22.7 percent HIV/Aids rate in adults and an economy dependent on South Africa, which surrounds it completely.

The small kingdom was plunged into crisis in 2014 when soldiers attempted to oust then-prime minister Thomas Thabane. Thabane fled to South Africa, where he spent two years, while the regional bloc SADC stepped in to end the crisis. Early elections took place the following year.

Thabane's All Basotho Congress (ABC) party took an early lead Monday after more than half of the votes had been tallied. Incumbent prime minister Pakalitha Mosisili's Democratic Congress (DC) party was trailing behind.

Final results are expected later in the week.