Commons public accounts committee chair Edward Leigh told Mr Nicholson at a meeting to discuss the contract's value for money that the committee's report, due in the autumn, will be 'damning'.
It follows a hard-hitting report from the National Audit Office last month, which said the£715m contract had failed to improve productivity and patient care.
Despite consultants' pay rising by 27 per cent to£110,000 a year, they were not providing more flexible care or spending more time with patients, it found.
But Mr Nicholson, giving evidence as a witness, said it is too early to judge the contract.
He told the committee: 'We don't operate a Soviet-style system where we can issue instructions from the top and get them delivered locally.
'To expect everything to happen at the beginning is a big ask, there are huge cultural changes here.'
Ways of measuring productivity are 'crude' and some trusts are struggling to implement the contract because of deficits and their own 'incompetencies', he added.
When asked whether managers have received adequate support from the Department of Health, he said they had. 'There are lots of ways the DoH has helped, but change takes experience and knowledge.'
He disagreed with the NAO finding that 84 per cent of trusts felt the contract was not adequately funded, saying the NHS always wants more money than is available. Although the NAO claimed it had identified£150m underfunding, the contract had only been underfunded by£90m, and this money had been handed over to trusts, he said.
However, he admitted that the contract should have been piloted, which did not happen because the British Medical Association wanted to bring in changes quickly, he said.
Labour MP Iain Wright said the consultants' attitude was similar to trade unions in the 1970s, which 'were very strong in negotiating pay deals with less work'.
Mr Nicholson also admitted that consultants were not carrying out as much out-of-hours care as was originally envisaged.
Labour MP Sadiq Khan asked whether the consultant contract, taken with the GP contract and Agenda for Change, showed the DoH had been 'over-indulgent'.
Mr Nicholson responded: 'We have not always got it absolutely right, particularly because a lot of the data we worked with was not of the highest quality.'