GPonline reported in November last year on DH plans to increase employers contributions under the NHS pension scheme as part of plans to shift £35m in administration costs to provider organisations.
The move is similar to the process that will see GP practices' CQC fees rise seven-fold over two years by 2017.
A government response published on Friday after a consultation on the proposed pension levy says: 'The DH will proceed to introduce a levy of 0.08% of pensionable pay from 1 April 2017.
'Scheme regulations will be finalised and laid before parliament in March. The levy will be collected at the same time as the standard employer contribution. In practical terms this means the employer contribution rate will increase from 14.3% to 14.38% from 1 April 2017.'
GP practices should not face additional costs, the government says, because the cost of the levy was factored into the 2017/18 GP contract deal, which included increases to cover rising expenses.
GPC deputy chair Dr Richard Vautrey told GPonline that the BMA would rather the costs had not been transferred to practices - much as GP leaders have opposed plans to shift the costs of running the CQC to provider organisations.
But he said: 'In terms of the impact on practices the extra cost will be recovered through [extra funding for] expenses.
'We were aware of the extra costs that were either going to hit practices or were already were hitting them, which is why we dealt with indemnity, CQC costs and even business levies as part of the contract deal.'
Dr Vautrey said he was confident that financial support for these increased practice costs could be maintained over time once initial funding had been agreed. 'Once we have secured that funding it is embedded within global sum payments and will not be removed,' he told GPonline.