A catalogue of failures by Nato warships and European coastguards led to the deaths of dozens of migrants left adrift at sea, according to a damning official report into the fate of a refugee boat in the Mediterranean whose distress calls went unanswered for days.

A nine-month investigation by the Council of Europe – the continent's 47-nation human rights watchdog, which oversees the European court of human rights – has unearthed human and institutional failings that condemned the boat's occupants to their fate.

Errors by military and commercial vessels sailing nearby, plus ambiguity in the coastguards' distress calls and confusion about which authorities were responsible for mounting a rescue, were compounded by a long-term lack of planning by the UN, Nato and European nations over the inevitable increase in refugees fleeing north Africa during the international intervention in Libya.

The Guardian first exposed the tale of the "left-to-die" migrant vessel in May last year, after gathering testimony from the voyage's few survivors. Having set sail from Tripoli in the dead of night, the dinghy – which was packed with 72 African migrants attempting to reach Europe – ran into trouble and was left floating with the currents for two weeks before being washed back up on to Libyan shores. Despite emergency calls being issued and the boat being located and identified by European coastguard officials, no rescue was ever attempted. All but nine of those on board died from thirst and starvation or in storms, including two babies.

The report's author, Tineke Strik – echoing the words of Mevlüt Çavusoglu, president of the Council of Europe's parliamentary assembly at the time of the incident – described the tragedy as "a dark day for Europe", and told the Guardian it exposed the continent's double standards in valuing human life.

"We can talk as much as we want about human rights and the importance of complying with international obligations, but if at the same time we just leave people to die – perhaps because we don't know their identity or because they come from Africa – it exposes how meaningless those words are," said Strik, a Dutch member of the council's committee on migration, refugees and displaced persons, and the special rapporteur charged with investigating the case.

The incident has become well known due to the harrowing accounts of the survivors, but the report makes clear that many similar "silent tragedies" have occurred in recent years. Last year a record number of migrant deaths were recorded in the Mediterranean. "When you think about the media attention focused on the [Costa] Concordia and then compare it to the more than 1,500 migrant lives lost in the Mediterranean in 2011, the difference is striking," Strik said.

Despite Nato's initial claim that none of its ships received a distress signal regarding the migrant vessel, the report reveals that distress calls were sent out by the Maritime Rescue Co-ordination Centre (MRCC) in Rome and should have been passed on to at least one ship under Nato command – the Spanish frigate Méndez Núñez, which was in the immediate vicinity of the migrant boat and equipped with helicopters. A rescue would have been "a piece of cake", said one Nato official.

"Nato declared the region a military zone under its control, but failed to react to the distress calls sent out by Rome MRCC," the report says. It claims that Nato's high command in Naples failed to pass on the distress messages to its naval assets in the area, but points out that the Spanish ship should still have received subsequent emergency calls that were broadcast on different satellite networks by the Rome MRCC.

According to the report, another naval vessel, the Borsini, an Italian warship that was not under Nato command at the time, was also positioned close to the migrant boat when the distress calls went out. As well as Nato, the flag states of the two ships concerned, Spain and Italy, also come in for heavy criticism by the rapporteur.

The report, which will be presented to the Council of Europe's parliamentary assembly on Thursday and has been seen in advance by the Guardian, concludes that the deaths of 61 migrants on board the boat, plus two more who died soon after reaching land, "could have been avoided", and censures Nato and its member states for not co-operating fully with the council's investigation.

"Many opportunities for saving the lives of the persons on board the boat were lost," it states, before going on to demand an overhaul of search-and-rescue procedures in the Mediterranean. Those who died "could have been rescued if all those involved had complied with their obligations", the report continues, adding that Nato and its individual member states should now hold their own inquiries into the incident and allow the full facts to come to light.

Abu Kurke Kebato, one of the survivors, said he hoped the report would pile pressure on Nato and the European community to unravel why so many of his friends were left to die. "I can't sleep, even now," said the 24-year-old Ethiopian, who is now waiting on an asylum claim in the Netherlands. "Every night I can see exactly what's happening once again, the hunger, the thirst, the falling [dying]. These powers, they knew we needed help and they did nothing. They must face justice."

The identity of a military helicopter that briefly flew over the migrants, offering them food and water and motioning at them to remain in place only to then fly off and never return, is still unknown.

On the 10th day of their ordeal the migrants drifted up to a large military vessel – so close that the survivors claim those on board were photographing them from the deck as they held up the dead babies and empty fuel tanks in a desperate appeal for assistance – but this too has not been definitively identified.

The report concludes that the military vessel must have been under the command of Nato, adding: "Nato must therefore take responsibility for the [military] boat ignoring the calls for assistance from the 'left-to-die' boat."

Strik said: "This report is only the beginning. The Mediterranean is one of the busiest seas on the planet, yet somehow nobody managed to rescue these migrants. We need more answers and I will continue to look for them. These people did not need to die and those responsible have to be called to account."

In response to questions from the Guardian, Nato said in a statement: "Clearly, this was a very tragic incident. However, as Nato has informed the Council of Europe rapporteur, there is no record of any aircraft or ship under Nato command having seen or made contact with the migrant boat in question, though a number of other search-and-rescue missions were executed by those ships and aircraft, including in the days preceding and following this incident.

"On 27 March, Nato received a general notice from the Maritime Rescue Co-ordination Centre in Rome of a small boat probably in difficulty, which requested to advise of any sighting of the boat in question. This was forwarded, according to usual practice, to all vessels under Nato operational control in the area."

In a letter to the Council of Europe inquiry, Spain's defence ministry claimed the Méndez Núñez had not received any communication about the migrant boat – contradicting Nato's claims –and referred other questions to Nato.