In major reforms of the social housing sector, the National-led Government is transferring thousands of state houses to NGOs, iwi and charities.
The first tranche of sales are taking place in Invercargill and Tauranga, where up to 2000 properties will be sold.
That process hit a hurdle on Friday, when Ministers confirmed that the PACT group had withdrawn from the process to buy and manage 348 state houses in Invercargill.
Tonight, Finance Minister Bill English said Mr Twyford's comments on the data he received were incorrect.
The costs were spread over a number of agencies between 2010 and 2016, including HNZ, Obie, MSD and Treasury, Mr English said.
They covered a range of activities including building more social houses, social housing valuation, and the transfer of houses to the government-owned Tamaki Regeneration Company.
"Treasury incurs the transaction-specific external costs for the process of transferring HNZ houses to community housing providers in Tauranga and Invercargill. These costs for the transaction process to the end of March 2016 were $2,198,478 - less than 10 per cent of the total amount cited by Mr Twyford," Mr English said.
"The bulk of the costs cited by Mr Twyford relate to the shift in housing assessment from Housing NZ to MSD in 2014, creating a one-stop shop for welfare and housing support, and in developing the social housing valuation supporting investment in better outcomes for tenants," Mr English said.