One source said the attack took place on Wednesday night after attackers detonated two Humvee bombs.
The Afghan Defense Ministry confirmed 43 soldiers were killed in a Taliban-claimed twin auto bomb and gun attack early Thursday.
The Taliban claimed responsibility for the attack in a media statement.
The report comes as similar attacks occurred in Paktia and Ghazni provinces on Thursday which left more than 69 people killed or injured.
"India strongly condemns the barbaric attack today at the Afghan National Army base in Kandahar province". Ministry spokesperson, Daulat Waziri, however, confirmed the attack.
The Taliban have been waging an insurgency for a decade and a half in an attempt to overthrow the government in Kabul.
The official, who was speaking on condition of anonymity, said the militants failed to overrun the base as reinforcement arrived at the scene.
Taliban attacks on Afghan military and police compounds have increased this week after USA officials met in Oman with delegations from Afghanistan, Pakistan and China to discuss the possibility of restarting peace negotiations with the insurgent group.
Standing at a post overlooking Afghan villages across the border, Zakaria said troops and paramilitary forces had defeated militants by launching several operations in the troubled region, which was a longtime stronghold for al-Qaida and the Taliban, as well as criminal gangs.
The attacks come just two days after Taliban gunmen stormed a police training centre in the eastern city of Gardez, killing at least 74 people.
They said the attackers detonated at least one explosive-packed Humvee vehicle and razed the compound in the early morning assault.
But the Taliban and other insurgent groups have also seen their areas of control or influence increase slightly from about 10 percent to 11.1 percent.