Azimi denied the Taliban claims saying: "Our soldiers travel by military convoy, not in civilian buses. And we have military air transportation."
Al Jazeera's Dan Nolan, reporting from Kabul, the capital, said that there were several different versions of events and it was difficult to verify the truth as journalists are unable to travel to the area because of poor security.
"The police chief in Kandahar says that two buses were attacked on the way from Kandahar to Helmand a few days ago," Nolan reported.
"He says it was a Taliban ambush, that the first bus was able to escape with minor casualties, but the second bus was not. It was hijacked by the Taliban and 50 passengers were taken hostage.
"Now they have reports of 24 dead bodies, that another 18 are still missing. They believe that there are another 18 bodies still to be found," Nolan said.
"A Taliban spokesperson gives a very different version of events ... he told Al Jazeera that they did hijack a bus but they took 27 hostages and they were all Afghan national army soldiers.
"The spokesman for the Taliban said that they were travelling on a civilian bus because they were too scared to travel through this area in an army convoy."
'Operating without fear'
Dawood Sultanzoy, an Afghan MP, told Al Jazeera that he had spoken to a source in Helmand, where one of the men wounded in the attack was being treated in hospital.
"I was told they were all civilians and they were on their way to Iran for work. They were stopped and they were told they were the militias for the governor of Helmand, therefore they would be killed," he said.
"This shows that the Taliban are always a few steps ahead in how brutal they can become and are operating without any fear."
On Wednesday, Taliban spokesman Ahmadi told Al Jazeera that the group had captured "at least 180 Afghan soldiers".
He said the the soldiers were seized while travelling in three buses on their way to Lashkar Gah, the capital of Helmand province.
Ahmadi said that the soldiers were dressed in civilian clothes and were on a mission to reinforce government troops in the area, "to prevent the fall of Lashkar Gah into the hands of the Taliban".
Violence in Afghanistan this year has killed more than 5,100 people, mostly suspected Taliban fighters, according to an Associated Press news agency count of figures from Afghan and Western officials.