Two Latvian men were arrested in the early hours of Thursday after they were discovered inside the perimeter of RAF Molesworth, a Cambridgeshire base used by the US military and Nato for intelligence operations.

The men, 32 and 36, were picked up at 2am inside the base, in an investigation that began four hours earlier when military police discovered an abandoned vehicle outside the facility.

Military police, helped by officers from Cambridgeshire police, discovered a small hole in the perimeter fence before finding and arresting the men, initially on suspicion of trespass on a prohibited site and causing criminal damage.

The suspects, Latvian nationals currently resident in the UK, were then further arrested on suspicion of an offence under section 4 of the National Security Act 2023 – namely entering a prohibited place for a purpose prejudicial to the UK.

Counter-terror police are now leading the investigation due to the nature of the incident, which comes a few days after the US withdrew B-1 bombers from RAF Fairford in Gloucestershire amid concerns about a possible Iran-directed attack.

Commander Helen Flanagan, head of counter-terrorism policing London, said there was nothing at this stage to suggest a connection to September's incident near RAF Fairford, but said investigators were yet to determine what the men had been doing.

"Our investigation into this incident is at its very early stages. A big part of this is looking at any potential motivation as to why the men were present at the site, but I must stress we are keeping an open mind at this stage and inquiries are very much ongoing," she added.

The abandoned vehicle was taken to a nearby police location. Initial searches led concerned officers to call in explosives specialists to carry out further checks, though nothing concerning was understood to have been found.

A police cordon was also briefly imposed on part of the A1 south of Peterborough and around the village of Glatton, as a precaution, but has been lifted. Officers were carrying out two searches at addresses in the Peterborough area in connection with the investigation, counter-terror police added in a statement.

Both men remained in police custody on Thursday.

RAF Molesworth is home to Nato's Intelligence Fusion Centre, which provides military intelligence to Nato, and the US Joint Intelligence Operations Center, Europe, which provides similar service for the US military's European command, though not Centcom, which is responsible for Iran.

The head of the armed forces, Air Chief Marshal Sir Richard Knighton, said he had "confidence around the safety and security of our bases" as he visited troops on a military exercise in Wales earlier on Thursday.

The chief of defence staff cited the "enormously close relationships from an intelligence perspective and operationally with the US" as reasons for his confidence, but said the US had removed its bombers from Fairford as a precaution.

"The decision to remove the bombers, which don't ordinarily live there … to take them back was an operational decision to reduce the risk," he added. The bombers were suddenly redeployed on Sunday, amid reports that the US feared Iran could orchestrate a drone attack on B-1 planes on the ground.

British sources remain sceptical that Iran would have the capability to launch an attack of such sophistication, though the investigation into why five men driving three white vans descended on a village next to Fairford continues.

Mark Rowley, the Met police chief, said the public would "see more progress on this investigation", and urged them to trust the police as they worked with spy agencies MI5, GCHQ and intelligence partners internationally.

The five men arrested near RAF Fairford, all British nationals in their 20s from London, have been released on police bail without charge, as has a sixth, a dual UK-Iranian national, who was arrested subsequently. A seventh man, aged 22, who was arrested on Wednesday on suspicion of preparing terrorist acts, was also let out on bail on Thursday.

Rowley acknowledged the threat landscape appeared to have changed. "We're dealing with an increased tempo of terrorists and also of threats that are directed by foreign states such as Iran and Russia," he said in a radio interview.