Mr Hammond, speaking in Edinburgh, said that defence plants in Scotland would no longer be able to bid for the bulk of Ministry of Defence contracts if Scots voted yes to independence.
He said the discussions about the country's constitutional future ahead of the poll on September 18, 2014 has caused uncertainty.
Mr Hammond added that independence would mean a complete end to major warship building on the Clyde - costing thousands of shipyard jobs.
He explained this was because the UK did not build such complex vessels abroad and there was "absolutely no plan to change that posture."
Even having the debate was causing damage, he warned during a visit to the Edinburgh facility of Selex ES. The electronics firm is part of a wider conglomerate part-owned by the Italian Government.
He said: "The nationalists have created a high degree of uncertainty with their plans, blighting the futures of thousands of families across Scotland.
"By their unwillingness to publish detailed defence proposals, they are doing nothing to dispel those concerns or allay the fears they cause."
The SNP insist their plans for a £2.5 billion budget would create defences better suited to the country's needs and Scottish Veterans Minister Keith Brown had challenged Mr Hammond to debate the issue with him.
The Defence Secretary rebuffed that, saying: "If Keith Brown wants a debate tell him to rebut everything in this report."
Mr Brown responded later: "That's strike two. First David Cameron runs away from a debate with Alex Salmond and now it appears Philip Hammond does not have enough confidence in his figures to debate them with me. It's typical - fly in to deliver a speech and a couple of hours later rush back to London."
The Conservative Minister claimed recruitment could be a problem for Scottish forces, compared with the range of opportunities in the British military. He said: "You have to question what sort of opportunities Scottish defence forces would offer by comparison."
Angus Robertson, the SNP's defence spokesman, responded: "An independent Scotland will have the defence capabilities and requirements for the 21st century."