US Apache helicopters killed at least 14 unarmed civilians in a series of previously unreported "gun runs" in eastern Baghdad only four days after the notorious killing of two journalists and 10 other civilians that was captured on a leaked cockpit video released in April.

The footage obtained by the WikiLeaks website led to the arrest of Iraq-based US army analyst Bradley Manning, who is accused of being its source. Posted on YouTube, the 39-minute cockpit video shows three incidents in which people were targeted as they walked along Baghdad streets, sat in a van or went into a building, unaware that gunships were aiming to destroy them. Because the dead included two Iraqi journalists working for Reuters TV the US authorities mounted a rare investigation.

War logs examined by the Guardian reveal that a bigger incident with a greater number of casualties occurred in a neighbouring part of Baghdad four days later on 16 July 2007. This time the Apaches were aided by unmanned surveillance drones and two F-16 fighter-bombers as US ground troops stepped up operations in densely populated eastern Baghdad against militants loyal to the anti-occupation cleric Moqtada al-Sadr. When it was over a local Iraqi informer told a US army interpreter that 14 civilians were dead, according to a military intelligence report.

The bloody incident begins after two foot patrols from A Company of the 504th Parachute Infantry Regiment come under small arms fire. One patrol "clears" the nearby Islamic Bank and then comes under fire again from a building belonging to the electricity ministry. Ten minutes later the other patrol reports fire from small arms and rocket-propelled grenade launchers. Two Apache helicopters are called in, known in US military jargon as Crazyhorse elements 20 and 21, and both "engage the AIF" (anti-Iraqi forces). (The helicopter involved in the shooting four days earlier was Crazyhorse 18.)

Ten minutes later one of the helicopters fires at two more AIF targets and reports it is being shot back at. An Iraqi army patrol arrives with a US training team. A US foot patrol from A Company reports that a nearby mosque is calling insurgents out to attack the Americans. No source is given, but the patrol may have an Iraqi interpreter who can understand the voice from the minaret.

The helicopter pilots spot a crowd gathering who are described as "possible AIF". The second helicopter, Crazyhorse 21, "conducts final gun run" to strafe unnamed targets that the intelligence report does not specify. By now two F-16 fighter-bombers are on station along with an unnamed drone that is filming the scene. Four Bradley armoured vehicles full of US ground troops are at the ready nearby.

But there is no more firing from the Iraqis and the drone's video footage, which is being monitored by US controllers, shows people coming out of the mosque and dispersing. "No weapons were seen." US troops remain on the scene for another 50 minutes before returning to base.

It is not their practice to remove or identify bodies. If done at all it is usually left to Iraqis. In this case the war log on the incident ends with what are described as unconfirmed reports of casualties. An Iraqi colonel says 12 AIF are dead. A named Iraqi informer on the ground rings the Parachute Infantry Regiment's interpreter and tells him 14 civilians are dead.

It is not clear whether both men are referring to one group of dead with differing estimates of whether they were insurgents or civilians, or whether there were separate groups totalling 26.

The terseness of the war log, which was compiled some time after the event, conveys little drama – which is why the cockpit video released by WikiLeaks in April is so important. It shows the true face of war as pilots treat a small densely populated corner of a foreign city as a battle space in which any adult male they spot is suspected of being a gunman.

Even so they are not supposed to kill unless they or any ground troops they are assisting have come under fire, or they are sure a person seen to be carrying a gun is about to fire at US troops.

If rules of engagement are broken the war logs usually conceal it. This appears to have happened with the killings illustrated in the leaked cockpit video. The Guardian has examined the secret intelligence reports for 12 July 2007 and compared them with the recorded words of the pilots and ground commanders. Parts of the video recording already showed the helicopter pilot and gunner giving false information to their commanders in order to get permission to fire. The logs show clear evidence of a cover-up after the event.

Take the second round of shooting in the 38-minute sequence. It revolves around a dark-coloured minivan that approaches a wounded man lying by the pavement and trying to drag himself to his feet. Two men jump out and go to his aid. Neither is carrying a weapon. They pay no attention to the bodies lying several yards away. Yet the cockpit recording has their commander saying "they have individuals going to the scene, looks like possibly uh picking up bodies and weapons". The helicopters get permission to blast the van regardless, even though firing on people who are aiding casualties violates US rules of engagement and international law.

The intelligence report of the incident says Crazyhorse "engaged AIF". In fact there is nothing seen by the helicopter pilots to show the men are insurgents. Indeed, when US ground troops reach the shot-up van a few minutes later they discover its passengers include two small girls who have been wounded, suggesting it was an innocent civilian vehicle that had rushed to help the wounded victim because it was the nearest transport available.

The third bout of gunfire from the helicopters comes when they destroy a large building on a street corner with three Hellfire missiles. Before firing the first one the pilot says: "There are at least six individuals in that building with weapons." The cockpit video has shown only one man going into the building, carrying something that might be a weapon. Two clearly unarmed men then go in and another unarmed man walks past the entrance seconds before the gunner launches his missile. Over the next few minutes the helicopters fire two more missiles in order to destroy the building completely.

As untrue as the helicopter pilots' live reporting was, the intelligence summary they filed later compounds the lies. Now the alleged gunmen are said to have been running into the building – clearly more suspicious behaviour than walking.

In the report's own laconic language: "1125: Crazyhorse engaged with 3xMissle 6XAIF with wepons that ran into a building at Grid MB 5514 8626. Building destroyed 6x AIF KIA".