John Healey flew into Cyprus on Wednesday night to calm the diplomatic fallout over a drone that evaded detection and hit an RAF base, prompting fury from local ministers.

UK officials believe a drone that hit an RAF base in Cyprus evaded detection by flying low and slow when it was launched by pro-Iranian militia in Lebanon or western Iraq.

But an investigation has been unable to establish conclusively where the Shahed-type drone was launched from. The attack occurred during the Iranian retaliatory bombardment over the weekend after the US and Israel launched a wave of strikes on Iran, killing the country’s supreme leader, Ayatollah Ali Khamenei.

The defence secretary’s visit comes amid a backlash in Cyprus over the drone attack on RAF Akrotiri, which has led to the evacuation of families living on the bases and a bolstering of its defences.

The attack on Sunday, and the two others intercepted later on Monday morning, are likely to have been launched by the Shia militia group Hezbollah, which is backed by Iran.

The drone, a cheaply made Iranian design, is used as a one-way attack vehicle. Though there were no injuries and damage was limited, the attack and the failure to stop the drone hitting the base has prompted anger from the Cypriot government. The Cypriot defence minister met Healey on Wednesday morning in Nicosia.

The drone strike was the first against a British military installation at the bases on the island in 40 years. Keir Starmer, the prime minister, has said the drone was launched before the UK announced on Sunday evening that it would allow the US to use two of its bases for defensive action against Iran. No RAF bases on Cyprus are being used by US bombers.

The Cypriot high commissioner in the UK, Kyriacos Kouros, said the country was “disappointed” with British failures to warn people on the island of the impending strike.

“Let’s say the people are disappointed, the people are scared, the people could expect more,” he told BBC Newsnight. “More cooperation with the government of Cyrus to safeguard that such incidents won’t happen again.”

On Monday, Cyprus’ president, Nikos Christodoulides, openly criticised the failure to stop the drone and said the country had no intention of participating in any military operation.

“This is something that we must say we view with dissatisfaction,” the president’s spokesperson, Konstantinos Letymbiotis, said on Tuesday, adding that there was “no clear clarification that the British bases in Cyprus would under no circumstances be used for any purpose other than humanitarian reasons in Sunday’s statement by the UK prime minister”.

He added: “All necessary steps will be taken to communicate our dissatisfaction, both with the way this message was communicated and the fact that yesterday there was no timely warning to citizens of Cyprus living near the Akrotiri bases.”

The UK has sent a Royal Navy destroyer – HMS Dragon – which is expected to arrive in Cyprus next week, alongside two Wildcat helicopters with counter-drone capabilities. Defence sources said the Wildcats would improve the ability to spot and intercept the type of low-flying drones which evaded detection on Sunday night.

Both France and Greece have deployed military support to the country including F-16 fighter jets and anti-missile and anti-drone systems. Families have been evacuated from RAF Akrotiri and several other areas. They are expected to remain away from the base for some time.