The Royal Navy's new multibillion pound hunter-killer submarine, HMS Astute, has been beset by design and construction flaws that have raised doubts about its performance and potential safety.

The Guardian can reveal that Astute, the first of seven new submarines costing £9.75bn, has been unable to reach its intended top speed.

At the moment, the boat, heralded as the most sophisticated submarine ever built for the navy, cannot sprint to emergencies or away from an attack – an essential requirement for a hunter-killer boat.

It would also be incapable of keeping pace with the Royal Navy's new aircraft carriers, which will be able to travel at more than 30 knots and need the submarines to protect them. One source told the Guardian the boat had a "V8 engine with a Morris Minor gearbox".

Other problems that have affected the boat in recent months include:

• Flooding during a routine dive that led to Astute performing an emergency surfacing.

• Corrosion even though the boat is essentially new.

• The replacement or moving of computer circuit boards because they did not meet safety standards.

• Concern over the instruments monitoring the nuclear reactor because the wrong type of lead was used.

• Questions being raised about the quality and installation of other pieces of equipment.

• Concern reported among some crew members about the Astute's pioneering periscope, that does not allow officers to look at the surface "live".

The MoD confirmed Astute had suffered some "teething problems" during sea trials. "It is normal for first of class trials to identify areas where modifications are required and these are then incorporated into later vessels of the class," a spokesman said.

Though the MoD said it cannot discuss the speed of submarines, the spokesman said Astute would "provide an outstanding capability for decades to come".

However, if the propulsion problems persist, they would represent one of the biggest procurement disasters the MoD has ever had to deal with, and potentially leave the Astute fleet struggling to perform all the duties it was built for.

John Large, an independent nuclear safety analyst and specialist engineer, said: "These problems are much more significant than the niggles and glitches expected to arise during working up of a new class of nuclear-powered submarine. Particularly disturbing is the apparent mismatch between the nuclear reactor plant and the steam turbine sets, putting the submarine speed below par and making her susceptible in the anti-submarine warfare theatre."

The shadow defence secretary, Jim Murphy, said ministers "must be clear over the impact of any problems with this essential programme on timing and cost".

Even though the boat has yet to start formal service, Astute – four years overdue and £2bn over budget – has been surrounded by controversy since it was first commissioned 15 years ago. In 2010, it was marooned off Skye, a calamity that led to its commander being removed from post. Last year a senior officer was shot dead by a junior member of the crew.

The Guardian has learned that during exercises off the east coast of the United States, a cap on one of the pipes that takes seawater from the back of the submarine to the reactor sprang a leak. A compartment began flooding with seawater, forcing the commander to surface immediately. Though nobody was hurt, an investigation revealed a cap was made from the wrong metal, even though construction records said the right metal had been installed.

The cap was supposed to have been "level one quality assurance". This means that BAE, which is responsible for building the boat, is supposed to give it the highest scrutiny.

"The fact the cap failed is bad enough, but the most worrying thing is that there is no way of knowing whether the submarine has other pieces of equipment like this on board," said a source. "The quality assurance tests are there to make sure this kind of thing doesn't happen, but it did. So what else has been installed that we don't know about? It is impossible to know. They fitted the wrong cap but it was still signed off."

The MoD confirmed that the incident had taken place. "During trials last year HMS Astute experienced a leak which was immediately isolated and the submarine returned safely to the surface," a spokesman said. "An investigation found one small part which had not been made of the correct material had corroded. A replacement was fitted at sea and the submarine continued with her programme. BAE Systems have carried out a full assessment which concluded all similar parts were fitted correctly."

Neither the MoD nor BAE was prepared to discuss how a cap made from the wrong metal had been fitted. BAE also declined to explain how it could be sure other parts were installed correctly when the quality assurance inventory system was proved to be flawed.

Some of the instruments which tell commanders about the state of the nuclear reactor were also feared compromised, the Guardian can reveal. The detectors which measure the power coming from the reactor are in a lead-lined water jacket that surrounds the reactor core.

The lead has to be "virgin" metal, mined from great depth, so that it does not carry any electrical charge of its own that could generate a false reading.

However, the lead used in Astute was not of the right quality, which means instruments gave incorrect readings. Using impure lead can also have a knock-on effect during maintenance – the charged metal can create increased and persistent radioactivity within the reactor compartment.

A source said this oversight was "unforgivable". Initially the MoD denied there was a problem with the reactor instruments. However, it then conceded the wrong lead had been used – but insisted tests showed the accuracy of the readings had not been affected. In addition, some of the small computer switchboards on Astute should have been placed six inches apart, but they were only one inch apart.

They did not conform to either naval or Lloyds civilian safety standards and are now having to be moved or replaced. The MoD says this work has been completed.

Of all the difficulties, it is the problems with propulsion which are the most sensitive. The MoD stated Astute would be able to make 29 knots, but the Guardian has been told it cannot do this.

Rather than building a new power plant for Astute, the MoD chose to use the Pressurised Water Reactor 2 (PWR2) from the much bigger Vanguard-class Trident submarines. It was linked to a steam turbine system based on the model used in the aged Trafalgar Class attack submarines.

"This was always likely to be a big problem, and so it has proved," said a source. "The PWR2 was meant for a much bigger boat, and Astute had to be designed around it. That may have cut costs, but it has caused problems. The power from the reactor does not translate into forward movement."

Large added: "So much promise was held out for the Astute class of nuclear powered submarine but these faults occurring during its commissioning into active/service, particularly in the propulsion system and its under-performance, suggest that the whole has been cobbled together from some ill-fitting parts – the real concern here is that these or similar mismatches will compromise nuclear safety at risk to crews and the public generally."

BAE Systems, which is responsible for building the Astute fleet, said: "Safety is of paramount importance to every stage of the design, build, test and trials of a submarine and is at the heart of everything we do. Before entering full service, every submarine is required to complete an exhaustive period of sea trials, which are designed to prove the vessel's capabilities. These trials also present an opportunity to improve performance by resolving any issues that may come to light during this time, which is not uncommon on a first-of-class submarine."

Read more: why Astute was trouble from the start