A guitar used by John Lennon has sold for $2.9m (£2.3m), setting what organisers have called a new world record for the highest-selling guitar at auction in Beatles history.

The 12-string Hootenanny acoustic guitar, used in the recording of the Beatles’ 1965 Help! album and film, had not been seen or played for more than 50 years.

The instrument had been owned by the Scottish guitarist Gordon Waller, known for being one half of the pop duo Peter and Gordon, who later gave the item to his band’s road managers.

Decades later, new owners living in the rural British countryside rediscovered the guitar in the midst of their move and put it up for auction with an estimate of between £485,000 and £647,000.

The guitar was bought through a telephone bid at the Hard Rock Cafe in New York on Wednesday as part of a two-day music icons sale by Julien’s Auctions.

David Goodman, the chief executive of the auctioneers, said: “We are absolutely thrilled and honoured to have set a new world record with the sale of John Lennon’s lost Hootenanny guitar.

“This guitar is not only a piece of music history but a symbol of John Lennon’s enduring legacy.

“Today’s unprecedented sale is a testament to the timeless appeal and reverence of the Beatles’ music and John Lennon.”

The guitar, made by the Bavarian firm Framus in the early 1960s, was seen in the Help! movie when the group perform You’ve Got to Hide Your Love Away.

It was also used during the recording sessions for Help!, It’s Only Love, I’ve Just Seen a Face and Girl, and on the rhythm track for Norwegian Wood played by George Harrison.

Darren Julien, the co-founder and executive director of Julien’s Auctions, said he had travelled to the UK to verify the guitar at the house it was being stored in and salvaged the original case, which had been thrown in a bin.

Julien said he had confirmed the instrument’s provenance via the Beatles historians Andy Babiuk and Danny Bennett.