The video, shot about a year ago, appeared to show military chaplains stationed in the US air base at Bagram discussing how to distribute copies of the Bible printed in the country's main Pashto and Dari languages.
In one recorded sermon, Lieutenant-Colonel Gary Hensley, the chief of the US military chaplains in Afghanistan, tells soldiers that, as followers of Jesus Christ, they all have a responsibility "to be witnesses for him".
"The special forces guys - they hunt men basically. We do the same things as Christians, we hunt people for Jesus. We do, we hunt them down," he says.
"Get the hound of heaven after them, so we get them into the kingdom. That's what we do, that's our business."
Questioned about the footage, Greg Julian, a US colonel in Afghanistan, told Al Jazeera: "Most of this is taken out of context ... this is irresponsible and inappropriate journalism.
"This footage was taken a year ago ... the Bibles were taken into custody and not distributed.
"There is no effort to go out and proselytise to Afghans."
Under the US military code of conduct, armed forces on active duty are prohibited from trying to convert a person's faith.
Ahmed Shah Ahmedzai, a former Afghan prime minister, told Al Jazeera from Kabul on Monday: "This is a complete deviation from what they [the US military] are supposed to be doing.
"I don't think even the US constitution would allow what they are doing ... it is completely against all regulations.
"This is very damaging for diplomatic relations between the two counties ... everyone knows people are very conservative here, very faithful to Islam. They will never accept any other religion.
"Someone who leaves Islam is sentenced very severely - the death penalty [is imposed].
"There must be a serious investigation now that it has come out into the public and [into the] press," he said.
Sayed Aalam Uddin Asser of the Islamic Front for Peace and Understanding in Kabul told Al Jazeera: "It's a national security issue ... our constitution says nothing can take place in Afghanistan against Islam.
"If people come and propagate other religions which have no followers in Afghanistan [then] it creates problems for the people, for peace, for stability.
Local language Bibles
The footage shot by Brian Hughes, a documentary maker and former member of the US military who spent several days in Bagram near Kabul, was obtained by Al Jazeera's Bays, who has covered Afghanistan extensively.
|It is not clear if the local language Bibles
were distributed to Afghans
In other footage captured at Bagram, Sergeant Jon Watt, a soldier set to become a military chaplain, said during a Bible study class: "I also want to praise God because my church collected some money to get Bibles for Afghanistan. They came and sent the money out."
It is not clear whether the Bibles were distributed to Afghans, but Hughes said that none of the people he recorded in a series of sermons and Bible study classes appeared to able to speak Pashto or Dari.
Hughes said: "The only reason they would have these documents there was to distribute them to the Afghan people and I knew it was wrong, and I knew that filming it … documenting it would be important."
Regulations by the US military's Central Command expressly forbid "proselytising of any religion, faith or practice".
But in another piece of footage, the chaplains appear to understand their actions were in breach of a regulation known as General Order Number One.
"Do we know what it means to proselytise?" Captain Emmit Furner, a military chaplain, says to the gathering.
"It is General Order Number One," an unidentified soldier replies.
But Watt says "you can't proselytise, but you can give gifts".
The footage also suggests US soldiers gave out Bibles in Iraq.
In an address at Bagram, Watt is recorded as saying: "I bought a carpet and then I gave the guy a Bible after I conducted my business.
"... the expressions that I got from the people in Iraq [were] just phenomenal, they were hungry for the word."
The video has surfaced as Barack Obama, the US president, prepares to host Hamid Karzai, Afghanistan's president, at a summit on Tuesday and Wednesday focusing on how to tackle the al-Qaeda and Taliban along the Pakistan-Afghanistan border.