The Spanish bank pulled out last week saying the already-delayed deal could not be completed by a revised deadline. It also said integrating RBS computer systems was proving difficult. However, Hampton said IT challenges could be overcome.
He hinted the rival lender had perhaps decided it was not a good time to be taking on new businesses.
Santander has yet to respond to his comments.
Meanwhile, Richard Branson's Virgin Money has expressed an interest in buying the branches.
State-backed RBS had been working on the £1.65 billion sale for more than two years, and the banks were understood to have planned to begin testing systems on November 1. The agreement, which would see the transfer of 1.8 million customers, was due to complete in the middle of next year.
The branches were predominantly in England, but included six proposed NatWest sites in Scotland.
The European Commission had called for their disposal as part of the UK Government's £45bn rescue of RBS in 2008. However, the union Unite has urged the Government to press the Commission to lift this requirement because of uncertainty over jobs.
Gail Cartmail, Unite's assistant general secretary, said: "This latest development represents another day of chaos for loyal RBS staff."