The BMA called the strike last week after being offered a deal that would see doctors receive a 3.5% pay rise this year, some expenses, including exam fees paid for, and an increase in the number of training posts.
The union said this was not enough, given that inflation is expected to rise, and that pay for resident doctors has not kept pace with inflation since 2008.
Writing in The Times, Sir Keir Starmer said: 'Walking away from this deal is the wrong decision. It is a reckless decision. And doing so without even giving resident doctors themselves the chance to vote on it makes it even worse.
'Because the truth is this: no one benefits from rejecting this deal.'
The 48-hour deadline is because the applications for these training posts, which start in the summer, would open in April so Thursday is the last day they can be added into the system, the government says.
In response, BMA resident doctor committee chair Dr Jack Fletcher told BBC Radio 4's Today programme that making 'threats about withholding jobs from doctors' at a time the NHS was already under strain, was clearly bad for patients.
'I don't think it's a realistic or credible way to end this dispute. It will end in a negotiating room,' he said.
He added that if the government were willing to offer a 'credible' deal, the action could be called off.
Resident doctors are due to walk out from 07:00 on 7 April to 06:59 on 13 April.
