Police said there was nothing so far to suggest the incident was linked to a suspected plot to attack a different air base in western England which had been used by US military to launch bombing missions against Iran.
The men were discovered after Ministry of Defence Police found an abandoned vehicle during a security patrol at RAF Molesworth, about 100km north of London and raised the alarm.
Subsequent checks found a small breach in the perimeter fence, and the men - aged 32 and 36 - were then arrested inside the base.
They were initially arrested on suspicion of trespassing on a prohibited site and criminal damage, then re-arrested on suspicion of "entering a prohibited place for a purpose prejudicial to the UK" under the National Security Act 2023.
Last month, several men were arrested over a suspected plot to attack Fairford air base, 145km west of London.
The government has linked the suspected plot to Iran, which has denied any involvement.
The incident raised concern about the security around the United Kingdom's military bases, particularly those used by US forces.
The United States said on Monday that a threat linked to Iran had prompted the removal of its bombers from Fairford.
"We're very aware of the recent heightened interest and concern around military sites, but at this stage there is nothing to suggest this incident is connected to the events at RAF Fairford last week," Helen Flanagan, head of Counter Terrorism Policing London, said in a statement on Thursday.
In relation to Thursday's arrests, police said they were also carrying out two searches at addresses in the Peterborough area in connection with the investigation.
An abandoned vehicle was recovered by police and later checked by bomb disposal officers, although nothing of concern was found, police said.
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