Responding to a DH consultation, the BMA reiterated concerns about 'completely unjustified' plans to raise pension contributions 142% from 2007/8 levels by 2014/15.
The BMA demanded a one-year freeze on 'rushed' plans to make practices pay employers' superannuation for locums.
Under DH proposals, the cost of employers' superannuation for locums - currently paid by primary care organisations - would be transferred into practices' global sum payments in England and Wales.
An average GMS practice in England or Wales would receive around £1,500. Practices would then be responsible for making employers' superannuation contributions for any locums they might employ.
BMA pensions committee deputy chairman Dr David Bailey warned that small practices - which are likely to need more locum cover - would be 'disadvantaged significantly' because the funding will be distributed on a capitation basis, rather than according to need.
He added: 'Locums who have already drawn their pension will be significantly cheaper to employ. This is going to skew the market.'
If the plans go ahead, it is vital for the money to be added to practices' global sum equivalent, so that all practices benefit, whether or not they receive MPIG top-ups to core pay, the BMA said.
The BMA called for clarity on how locums could check whether payments had been made by employer practices, and for more detail on how funding for the 40% of practices in England on locally agreed PMS contracts would work.
The BMA response warns: 'We also feel it will be impossible for practices to take on locums whilst taking on additional CCG responsibilities if the cost of the locum is not fully covered.'
A DH spokeswoman said: 'Our proposals are intended to make sure the payment arrangements are fair.'
BMA leaders said they were disappointed the government had 'gone back on' 2008 pension reforms that would save taxpayers up to £67bn by 2060.
NHS staff earning more than £110,000 a year will see contributions rise 142% between 2007/8 and 2014/15 while their benefits are cut, the BMA said.
Dr Bailey added that it was 'manifestly unfair' to ask NHS staff to pay 'around double the amount per pound for their pensions as civil service staff'.