Mr Lubbers, a centre-right prime minister from 1982-94, said they were stored underground in strong-rooms at the Volkel air base in Brabant.
He made the revelation in a documentary for National Geographic - saying: "I would never have thought those silly things would still be there in 2013."
The presence of nuclear weapons on Dutch soil has long been rumoured.
'Pointless'
However, Mr Lubbers is believed to be the most senior person to confirm their existence.
"I think they are an absolutely pointless part of a tradition in military thinking," Mr Lubbers said.
The Telegraaf newspaper quoted experts as saying the weapons held at Volkel were B61 bombs that were developed in the US in the 1960s. At 50 kilotons, they are four times the strength of atom bombs used on the Japanese cities of Hiroshima or Nagasaki at the end of World War II.
There has been widespread speculation about the presence of nuclear weapons or parts of them on Dutch soil for decades.
The "poorly kept secret" of the existence of nuclear weapons in concrete vaults emerged in 2010 in the classified US documents published by Wikileaks, reported NRC Handelsblad newspaper.
It was mentioned in a report on a conversation involving US Ambassador to Berlin Philip Murphy, US diplomat Phil Gordon and German Chancellor Angela Merkel's national security adviser, Christoph Heusgen.
In November 2010, then-Foreign Minister Uri Rosenthal declined to give any explanation to the Dutch parliament.
A spokesman for the Royal Dutch Air Force was quoted by Dutch broadcaster NOS on Monday as saying these issues "are never spoken of".
"[Mr Lubbers], as former prime minister, knows that well," he added.
Mr Lubbers said in the documentary that he first heard about the existence of the bombs when he was working for the air force at Volkel in 1963.
A colonel asked him how the bombs' existence could be kept secret, and Mr Lubbers advised him to give each nuclear weapon part a number so they would not attract attention, he said.
"And that's what happened", he added.
In October 1983, while Mr Lubbers' was prime minister, more than 500,000 protesters demonstrated in The Hague against the placement of US nuclear-armed Cruise missiles in the Netherlands.
The Oslo Times