He is appealing against the deregistration through the High Court at Hamilton, where a judge has ruled the penalty should be reassessed.
By last month the committee's investigation, tribunal hearings and High Court appeals related to the case had cost the Medical Council $967,000.
That figure will grow as the appeal continues and the tribunal reconvenes in Hamilton next month to review the penalty.
In June, the Medical Council sent a letter to the country's 13,874 practising doctors announcing a one-off disciplinary levy to cover the cost of the case, the most expensive taken by the council.
Its chairman, John Adams, said the council had a deficit of $1.29 million for the 2010-11 financial year, which included almost $1 million in the disciplinary fund.
Dr Adams said Dr Vatsyayann's case had been expensive for the council, as was another in 2007, where a doctor investigated for writing false prescriptions cost it $750,000.
He said the council had budgeted to break even in the next financial year but that was at risk if more costs were incurred in Dr Vatsyayann's case, and it needed to ensure financial stability.
"Accordingly, council has unanimously agreed to implement a one-off disciplinary levy on all doctors practising in New Zealand to be paid on all applications for a practising certificate in the 2012-13 financial year."
The $75 levy was implemented on July 1 for 12 months, taking the total disciplinary levy for that year to $195, and making the combined levy and application fee for a practising certificate $729.
"In making this decision, council was very aware of the cost burden this may have for some doctors."
Dr Adams said the council had looked at ways to reduce its legal costs in investigations of unethical conduct and had implemented in-house legal representation, which had helped.
He said 19 doctors had said they were upset at have to pay the levy.
"Some people, not understanding the process, felt that the person who was being prosecuted should be responsible for the costs."
General Practitioner Council chairwoman Kate Baddock said GPs had accepted the levy as reasonable, but she said there would be concern if it continued.
"If it was going to be a matter happening every year, we would have to re-look at the way the funding was used."
Dr Baddock said GPs recognised that tribunals could be expensive, and any doctor could face it at any stage.
THE GAP
Medical Council costs in case against Dr Suresh Vatsyayann
* To date: $967,286
* Imposed against doctor: $361,635
* Paid by doctor: $34,005.