While US diplomats were pulling bodies from a burning Libyan consulate and frantically smashing up hard drives last 11 September, their superiors blocked rescue efforts and later attempted to cover up security failings, according to damaging new evidence that may yet hurt Hillary Clinton's presidential hopes.

In vivid testimony to Congress on Wednesday, Gregory Hicks, deputy to murdered US ambassador Christopher Stevens, revealed for the first time in public a detailed account of the desperate few hours after the terrorist attacks on the US consulate in Benghazi.

He also said that Stevens went to Benghazi to beat a 30 September deadline to convert the mission to a permanent posting. There was additional time pressure because Clinton planned to visit Libya later in the year and to announce the opening of the post, Hicks said.

But Hicks and two other state department witnesses also singled out the government response for criticism. Until now that criticism had been largely dismissed as a partisan effort by Republican congressman to smear former Clinton, who was secretary of state at the time.

Hicks claimed Clinton's chief of staff, Cheryl Mills, telephoned him to complain that he had given critical evidence to congressional investigators without the presence of a "minder" from the state department. "A phone call from that senior a person is generally considered not to be good news," said Hicks, who said he had since been demoted. "She was upset. She was very upset."

The career diplomat also alleged he was actively discouraged by officials from asking awkward questions about why other top Clinton aides, including the UN ambassador Susan Rice, initially blamed the attack on a spontaneous protest that got out of control. He described that briefing he described as "jaw-dropping, embarrassing and stunning". It is now thought the attacks, involving up to 60 heavily armed militia, were co-ordinated by Ansar al-Sharia, a group affiliated to al-Qaida, and timed to coincide with the 11th anniversary of the attacks on the World Trade Center in New York and the Pentagon in Washington.

The allegations of a state department cover-up follow equally embarrassing claims that military leaders blocked efforts to dispatch special forces troops to the Benghazi consulate.

In testimony that first emerged on Monday, Hicks claims that four special forces soldiers with him in Tripoli were "furious" when they were told by superiors in Washington that they could not join a relief flight to Benghazi organised by the Libyan government in the hours after the initial attack.

Mark Thompson, a former marine who heads the foreign emergency support team, also alleged that the White House blocked his efforts to dispatch a specialist group from the US that is designed to respond to incidents such as the Benghazi attaack.

Hicks said he was told that US air force jets based in Italy could have reached the consulate in "two to three hours" but were blocked, out of fear of offending the Libyan government, and because a refuelling tanker could not be found.

Pentagon officials have repeatedly argued that none of the available military assets could have reached Benghazi in time to prevent the death of ambassador Stevens and three other consular staff. But Hicks insisted even if they had been too late, better attempts should have been made. "People in peril in future need to know that we will go to get them," he said. "That night we needed to demonstrate that resolve even if we still had the same outcome."

Hicks also rejected the defence given by Hillary Clinton when pressed on the initial delay in attributing the attack to terrorists, arguing the US undermined its Libyan allies who were rightly pointing to Ansar al-Sharia.

"President Magarief was insulted in front of his own people, in front of the world. His credibility was reduced. His ability to govern was [damaged]. He was angry … He was still steamed about the talk shows two weeks later. I definitely believe it negatively affected our ability to get the FBI team quickly to Benghazi."

Hicks also testified that part of the reason that Stevens was in Benghazi was to make preparations to convert the mission to a permanent post, and to lay the groundwork for a visit by Clinton. "At least one of the reasons the ambassador was in Benghazi was to further the secretary's wish that that post become a permanent constituent post" and because Clinton "intended to visit later that year" to announce the conversion.

Democrats on the committee attempted to play down the significance of the new evidence. "There is no smoking gun today," said Mark Pocan of Wisconsin. "There is not even a lukewarm slingshot." Deputy chair Elijah Cummings said the hearing would not be able to get to a full picture without recalling other military witnesses.

But the powerful and at times emotional testimony of the state department witnesses is likely to rekindle questions over the government's handling of the incident. The Obama administration had hoped that an earlier independent review panel had drawn a line under the issue.

Republicans characterise their refusal to let the Benghazi issue go as a determination to find out what went wrong. But some Democrats have suggested that the real intention is to taint both the White House and Clinton in a bid to dent her chances in 2016 should she decide to run.

Hicks described receiving the final telephone call from ambassador Stephens revealing he was under attack. He said an attaché ran into his villa "yelling Greg, Greg, the consulate's under attack". Hicks looked at his phone and had two missed calls. He called back and got ambassador Stevens. "He said, 'Greg, we're under attack.'"

"I said 'OK' and the line cut."

Hicks then described how he had taken refuge in a secure villa that was set alight with petrol by the attackers. He also told how the embassy building in Benghazi was hit by mortar fire and how a tiny group of soldiers at both sites fought through the night to prevent both facilities from being overrun.

"September 11 was a routine day until we heard the news that our embassy in Cairo had been stormed and they were trying to tear down the flag," recalled Hicks.

"I had bad cellphone reception but walked to the tactical operations centre and heard that our consulate in Benghazi had been breached and at least 20 armed individuals were in the compound."

After twice not recognising the number, he said he received a short call from ambassador Stevens, thought to be his last, who said they "were under attack". He and an assistant, Sean Smith, were led to a safe area inside a villa next to the consulate by security agent Scott Strickland. It was set on fire with jerry cans of fuel shortly after 9pm.

"Scott attempted to lead them out but they didn't follow. He tried to get back in but was beaten back by the smoke," said Hicks. "Petroleum-based fires emit cyanide gas and one full breath can kill you. They managed to pull Sean out, but he was dead. They couldn't find Chris."

A second wave was coming to attack and the remaining consulate staff fell back to a nearby CIA annex. "After about an hour and a half of probing attacks from terrorists that they were able to repulse they decided to evacuate," said Hicks. They met with a response team flown from Tripoli on a Libyan C130 transporter and retreated back to the capital.

Hicks says at this point he still thought that ambassador Stevens might be alive and he received word from the Libyan government that he was being held in a hospital run by the same group responsible for the attack. "I thought we might need a hostage response team to get the ambassador out of a hospital under enemy control," explained Hicks.

At the same time the group was claiming responsibility for the Benghazi attack on Twitter, embassy staff began noticing threats against their facility in Tripoli too.

"We began planning to evacuate, and took 55 people to the annexe," said Hicks. "At 2am Hillary Clinton calls and she asks me what is going on. I brief her mostly about ambassador Stevens and told her we would need to evacuate. At 3am I received a call from from the prime minister of Libya who told me that ambassador Stevens had passed away. It was the hardest call I have ever had to take."

Hicks says he has vivid memories of communications staff in Tripoli destroying classified equipment including a female officer manager "smashing hard drives with an axe". The contingent in Benghazi then tried to drive to the airport around dawn but were hit by two mortar rounds.

"The first mortar was long and landed among the Libyans who were escorting us – they took casualties. The next was short and landed on the annex roof, killing one of our people and seriously wounding another, David. Mark charged onto the roof and strapped David, who was a large man, to his back and carried him down the ladder."

Hicks says he wanted to send further reinforcements to Benghazi where they had been fighting through the night but was unable.

Eric Nordstrom, a security officer who also gave evidence to Congress said the lessons state department employees have taken from Benghazi were scathing: "Whether you're at a mission, preparing for a hearing or you're standing on top of a building "surrounded by a mob," he says, "The message is the same: You're on your own."

• This article was amended on 8 May 2013 to make clear that mortar attacks took place in Benghazi, not Tripoli.