Counter-terrorism police have arrested two Latvian men inside a Royal Air Force base in southeast England that houses United States and NATO intelligence operations, after a breach of the perimeter fence was discovered.

The men, aged 36 and 32, were arrested at RAF Molesworth in Cambridgeshire in the early hours of Thursday. Both are Latvian nationals residing in the United Kingdom.

A security patrol spotted an abandoned vehicle near the base late on Wednesday night. Police then found a small breach in the perimeter fence before locating and arresting the men inside the base.

The two men were taken to a police station in Cambridgeshire, where they remain in custody. They are being held on suspicion of trespass and of entering a prohibited place "for a purpose prejudicial to the UK".

Due to the nature of the incident, counter-terrorism police are leading the investigation.

Commander Helen Flanagan, head of Counter Terrorism Policing London, acknowledged the broader climate of concern. "We're very aware of the recent heightened interest and concern around military sites," she said.

However, she stressed there was no known link to a separate recent incident. "But at this stage there is nothing to suggest this incident is connected to the events at RAF Fairford," she added.

Flanagan said the investigation at RAF Molesworth is at an early stage, but that inquiries would focus on "any potential motivation as to why the men were present at the site".

RAF Molesworth, formerly a Second World War airbase, is now a non-flying facility managed by the United States Air Force. US intelligence has based its operation centres for Europe and Africa at the site near Huntingdon. It is also a NATO intelligence hub, according to a Central Intelligence Agency website.

The arrests come amid heightened concern over security at UK military installations following a major incident at RAF Fairford in Gloucestershire on September 27. During that incident, three suspicious vehicles were seen near the base, prompting a major incident to be declared and US military aircraft to be flown out abruptly.

Seven men, all in their 20s, were arrested in connection with the RAF Fairford incident. All have since been released on bail. One is a dual UK-Iranian national.

Police said nothing so far suggests any connection between the two incidents.