Ellis said the two-year ban was at the extreme end of the punishment scale, and tied in with the World Anti Doping Agency regulations for human dopers.
Ellis aid Reserpine is used for the treatment of hypertension, but it has elements in it which have it on the FEI banned list and should not be used around competition time.
Ellis first got word of the positive result late last night and described it as ''the worst phone call I've had in six and a bit years in the role, no question at all".
He said the timing was particularly bad for the sport, given that New Zealand eventing is on a high, with Andrew Nicholson the world No 1 rider, Paget ranked No 3 and coming on the back of the team bronze medal won at the London Olympics last year.
Between Nicholson and Paget, the pair won five of the six global four star rated events in the 2012-13 season.
''We are building towards the world championships (in France next year) and this knocks everybody, not just Jock," Ellis said.
If the B sample proves negative the issue ends and 29-year-old Paget would keep his Burghley title.
After winning Burghley, Paget described Promise as ''an exceptional horse who loves his job. It's taken me a while to work out how to have him prepared correctly for all three days. I think we're getting on to that now."