His 1965 track Tears was the third biggest-selling single of the decade, according to a newly compiled chart.
The Beatles occupy the top two places in the chart and have an additional three records in the Top 10.
DJ Tony Blackburn counted down the Top 60 best-selling records of the 1960s in a special programme on BBC Radio Two, broadcast on Bank Holiday Monday.
According to sales data compiled by the Official Charts Company, the biggest selling single of the 1960s was She Loves You by The Beatles.
I Want to Hold Your Hand, recorded by the Fab Four in 1963, came second.
The Unswinging Sixties
The other Beatles records in the Top 10 are Can't Buy Me Love at four, I Feel Fine at five and the double A-side We Can Work It Out/Day Tripper at seven.
Yet Dodd's track - which topped the UK singles chart for five weeks and was the biggest-selling single of 1965 - outsold them all.
"It comes as no surprise to see the Fab Four at number one, but other aspects of the chart are perhaps a little unexpected," said Blackburn.
Jeff Smith, Radio 2's head of music, called the chart "a nostalgic reflection of the enduring appeal of the music of the '60s and the artists that defined the decade."
Dodd, now 82, has been in showbusiness for more than 50 years.
Born in Liverpool in 1927, he is best known for his buck teeth and frizzy hair, tickling stick and his creation of the Diddymen.

The 93ft (28m) long VC10 fuselage left Bruntingthorpe in Leicestershire for RAF Museum Cosford, Shropshire, at about 07:00 BST. It will be on permanent display in the autumn.
The VC10 has been one of the RAF's most significant assets for nearly 50 years, the museum said.
A lorry took the fuselage on the M69, M6 and the M54 and through Shifnal in Shropshire.
The VC10 entered service with the RAF in 1966 and had the ability to carry up to 124 troops at a time with nine crew members or a freight load of up to 20,400 kg (44,974 lbs). It completed its final mission in 2013.
It will be positioned on the airfield at RAF Cosford for about five to six weeks and partially reassembled, before being moved on to the museum site in August.
It is scheduled to be placed on permanent display next to the Hercules in October.
The museum's head of collections, Ian Thirsk, said: "For one aircraft type to have been in service for such a long period is remarkable in itself.
"However, when this is added to the variety of roles and worldwide scope of operations, it is clear this is a unique aircraft."
Eccentric comedian Ken Dodd was one of the biggest recording artists of the 1960s, new research has revealed.
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A military aircraft has made a six-hour journey to its new home at a museum.