The Conservative minister said it would take at least 10 years and cost tens of billions of pounds to move the UK's nuclear deterrent from the Clyde.
His comments came despite colleagues in the Coalition Government saying they will not "pre-negotiate" the terms of any independence settlement.
The Ministry of Defence also insists it is making no contingency plans for a separate Scotland.
The SNP claimed Mr Hammond had let the "cat out of the bag" that ministers were considering how to move Trident.
Mr Hammond categorically rejected the Scottish Government's aim, contained in its independence White Paper, to rid Scotland of nuclear weapons by 2020.
He said technical challenges meant the UK's nuclear deterrent would have to stay on the Clyde until at least 2026.
"For technical and planning reasons it will take at least a decade - probably significantly longer than that," he said.
On the 2020 aim, he added: "This will be a process of negotiation.
"It is not a question of one side saying 'these are the terms' - it is a question of both sides sitting down and having a discussion. Neither side can unilaterally impose its aims."
Mr Hammond also insisted there would be no vacancy for the position of Prime Minister after a Yes vote in September.
He backed the retention of three naval ports - Faslane, Devonport and Portsmouth.
SNP Westminster leader and defence spokesman Angus Robertson said: "He has always said the Tories think the people of Scotland will vote No and the MoD is not spending any time on planning for independence. Yet today it is clear he is looking at a timetable in the event of a Yes vote."
The Scottish Government's independence White Paper describes the UK's nuclear deterrent as an "indiscriminate and inhumane destructive power", and says Scotland should be rid of Trident as soon as is "safe". But the paper leaves room for manoeuvre with the 2020 deadline an aspiration, not a pledge.
Meanwhile, on a visit to an engineering firm in Gloucestershire yesterday, David Cameron urged Scottish voters to stick with the "incredible family" of the UK.
He said: "Think of all the things this family of nations has done together, whether it's defeating Hitler or inventing the National Health Service or helping the poorest people in the world."
He warned the consequences of a Yes vote would be "very bad", adding: "I'm not simply saying the Scots would be better off inside the United Kingdom - we are all better off staying together as a family."
lClyde-built Type 45 destroyer HMS Dragon has been sent to track an unusually large Russian naval task force transiting the English Channel, amid a resurgence in Russian air activity. Her captain said it was unusual because a force of this size had not passed UK shores for some time.