The ministry did not give a breakdown of the casualties, many of whom were young recruits in training, in the hours-long attack near Mazar-i-Sharif city on Friday.
The US military has said that "more than 50" Afghan soldiers were killed, while an Afghan army source who was on the base at the time put the death toll as high as 150, with dozens more wounded.
The attacked military base is near the northern city of Mazar-e-Sharif Source: SBS
"They entered the compound using two army trucks with machine guns on top of them. They opened fire on everyone. And then they entered the mosque and dining room, killing everyone indiscriminately," Mohammad Hussain, an army officer wounded in the attack, said as he was treated in hospital.
Watch: Dozens of Afghan soldiers killed in the attack
"Their leader came in and shouted 'aim for their heads'. I jumped out of the window, my friends were killed," one 19-year-old soldier, Mohammad Qurban, told AFP from hospital where he was being treated for hand and stomach injuries.
Afghan President Ashraf Ghani flew to Mazar-i-Sharif on Saturday to pay a "courtesy visit" to wounded soldiers, as grieving families reached the base to collect flag-draped coffins bearing their loved ones.
Two of the attackers blew themselves up in the raid, which was claimed by the Taliban late Friday and which underscores rising insecurity as Afghanistan braces for an intense spring fighting season.
The defence ministry said Afghan forces had killed all the attackers, who witnesses said were dressed in Afghan army uniforms. At least one survivor who spoke to AFP speculated the militants must have had inside help.
The toll could change, the ministry said, adding it would provide more information once an investigation was completed.
Afghan officials have been known to minimise casualty figures in some major attacks on military sites, such as in early March when gunmen disguised as doctors stormed the country's largest military hospital in Kabul, killing dozens.
Officials put the death toll in that attack at 50, but security sources and survivors told AFP more than 100 were killed in the brazen and savage assault.
Military targets
The attack on the Kabul hospital in March came a week after 16 people were killed in simultaneous Taliban suicide assaults on two security compounds in the capital.
Atiqullah Amarkhail, an Afghan military analyst and retired general, said Saturday that Afghan forces must develop a counter-strategy for such attacks.
"It is a total intelligence failure. It keeps happening again and again. It is a guerrilla war, the militants attack in small groups and cause big damage. We should learn and counter their tactics," he said.
Afghan security forces, beset by killings and desertions, have been struggling to beat back insurgents since US-led NATO troops ended their combat mission in December 2014.
According to US watchdog SIGAR, casualties among Afghan security forces soared by 35 percent in 2016, with 6,800 soldiers and police killed.
More than a third of Afghanistan is outside government control and many regions are fiercely contested by various insurgent groups, as Kabul's repeated bids to launch peace negotiations with the Taliban have failed.
The US has around 8,400 troops in the country with about another 5,000 from NATO allies assisting a much larger Afghan force in the war against the Taliban and other Islamist militants.
Earlier this month the US military dropped its largest non-nuclear bomb on Islamic State group hideouts in eastern Afghanistan, killing nearly a hundred militants, according to unverified figures from Afghan officials.
The attack triggered global shockwaves, with some condemning the use of Afghanistan as what they called a testing ground for the weapon, and against a militant group that is not considered as big a threat as the Taliban.
