The Spanish prime minister has declared three days of mourning after at least 68 people were killed and dozens more injured in a collision between two high-speed trains that officials suggested was caused by an “inexplicable” error at the central command centre.

The trains, one from Spain’s state-owned Renfe and the other from the private rail company Iryo, were travelling on Wednesday morning in the same direction on the line that stretches from the Spanish capital, Madrid, to the southern region of Andalusia. After the Iryo train came to a halt, the other slammed into its rear, knocking several carriages off the track near the town of Urda.

The tragedy was the second major deadly high-speed train accident this year in Spain, rattling a country where the extensive rail network has long been a point of pride. “Today all of Spain is grieving,” the prime minister, Pedro Sánchez, said.

In January, 46 people were killed and dozens more injured after two trains – again, one from Renfe and one from Iryo – collided on the same line near the town of Adamuz in Andalucía. On Wednesday Sánchez said it was “unacceptable for a country like Spain to suffer two high-speed train accidents in the same year, as we have”.

The causes of the accident were under investigation, he added. If it emerged that it was due to failures in the security system or negligence, these shortcomings would be addressed with the “utmost severity”, he said.

The Urda crash, which ranks as one of Europe’s deadliest such disasters this century, comes weeks before general elections in which Sánchez is waging an uphill battle for re-election. The crash in January left his Socialist party fending off criticisms that it had not done enough to maintain the safety of the high-speed rail line, suggesting that this latest crash would add to the fractious political climate.

Images from the scene showed a derailed train with at least one carriage remaining on an elevated section of track. Twisted metal, broken panels and wreckage could be seen strewn across an embankment beneath the rail line. Officials said the trains had been carrying 544 people.

Spain’s transport minister, Óscar Puente, said that rear-end collisions like that which had taken place on Wednesday were “highly unlikely” and suggested that the accident may have been caused by human error made in “inexplicable” circumstances.

He said the LZB signalling system, which automatically halts a train if the line ahead is occupied, had gone down at about 8.30am local time due to a computer malfunction. As a result, an estimated six trains had been halted along a stretch of around 63km of track, he said.

The task of monitoring the rail lines then fell to a 24-hour command centre in Madrid. Minutes after the computer malfunction, the centre instructed at least two of the trains to continue as normal, despite the fact that there was still a “stop signal” in place, said Puente.

“It was the control centre, through its operators, that made the decision to resume traffic, under circumstances that, from our point of view, are inexplicable,” he said. “Clearly, it was a wrong decision.”

The Castilla-La Mancha regional government said on Wednesday afternoon that the death toll had risen to 68 as rescue teams continued to ⁠search through the wreckage of the derailed carriages. Castilla-La Mancha’s leader, Emiliano García-Page, told reporters that more victims were likely as “it has not yet been possible to reach the bottom of the carriages”.

Officials said another 107 people had needed medical treatment in hospital, including 15 who were in a serious condition.

Miguel, ‌a passenger travelling with several colleagues in the rear car of one of the trains, described the moment of the accident to Cope radio. “We heard a massive roar, a truly enormous thud that went on for 10 seconds, as if the train were ‌about to derail,” he said. “Through the right-hand window, we could see a wrecked train – I imagine it must have been the other one.”

The crash turned the municipality of Urda, surrounded by olive groves and vineyards, into a hub for the rescue effort. A local sports centre became a triage centre for those with minor injuries, while a nearby hall was repurposed into a space for those scrambling to find their missing loved ones.

A constant flow of vehicles from local, regional and national emergency services headed in and out of the town, while locals pitched in by bringing food and bottles of water to those waiting anxiously for news of their relatives.

Giving initial details about the crash, Puente said the Iryo train had been travelling ahead on the tracks and had been sitting stationary when the Renfe train was instructed by the command centre to resume its journey. The Renfe train then travelled approximately 25km before colliding with the Iryo train about 17 minutes later.

The speed at which the Renfe train had been travelling remains unknown, the transport minister told reporters, though the section of rail on which it was travelling allows for speeds of up to 200km/hour.

The control centre “had more than enough time to verify the error, and they did not fix it”, Puente added. “I am not attributing responsibility to anyone, I am just stating the facts.”

Puente said that similar erroneous instructions had been given to at least one other train on Wednesday morning. “And it was the engineer of one of the trains who corrected the command centre and told them he can’t resume normal operation – it has to be [an] on-sight operation,” Puente said, citing a protocol that allows trains to advance but at a greatly reduced speed in order to ensure that there are not other trains sitting on the tracks ahead. “The operator said: ‘OK, on-sight operation.’”

Amid growing anger over the crash, the prime minister said there was little to suggest that the two high speed rail collisions Spain has suffered this year had shared any kind of similar cause.

“Everything strongly suggests that the causes of the two accidents are completely unrelated, but it is not up to me to say so,” he said. “But what is clear is that, if we need – as we certainly do – to further strengthen safety in order to rebuild confidence in our high-speed rail system, it will be done.”

Across the country, people held moments of silence for those who were killed, while Spain’s football federation postponed all 24 Copa del Rey games scheduled for Wednesday.

The first victims to be named included a 31-year-old Guardia civil agent, José Manuel Chacón.

The national law enforcement agency expressed its “deepest condolences” to his family, friends and colleagues. Spanish media said the missing included a former minister for the People’s party and several foreigners who were likely on holiday in the country.

The opposition People’s party leader, Alberto Núñez Feijóo, called for an immediate investigation into what had happened, as well as a “complete and independent review” of Spain’s entire rail network. “Spain has the right to know what is going on with its infrastructure,” he told reporters.

Reuters and Associated Press contributed to this report