Hamish Meldrum, chair of the British Medical Association's General Practitioners Committee, said they had warned the Government that the target could not be met without more resources.
The Health secretary, John Reid, said GPs were "wrong" to refuse patients advance appointments. The Prime Minister appeared flustered on BBC1's Question Time last week when confronted by voters who could not make a doctor's appointment more than 48 hours ahead.
Dr Reid said: "In the course of last year we discovered thata very small number of GPs, about three per cent, believed either that they had to see everyone within 48 hours - mistakenly - or believed they couldn't run a system that had forward bookings and a 48-hour priority. In both of these cases they were wrong."
But Dr Meldrum told The Independent on Sunday that the problem was caused by a lack of doctors and nurses. "By skewing it one way you put pressure on the system in another place," he said. "Right from the beginning we weren't keen on this target. The basic problem is we don't have enough doctors or nurses. In some areas we just can't recruit."
Dr Reid highlighted Labour's plans to give pregnant women more choice over where and how they had their baby. He contrasted that with Conservative plans to "divert" £1.2bn of NHS money to patients using private healthcare.
"It will mean longer NHS waits, longer waiting lists, and it will mean lives being put at risk," he said. "These Tory cuts will be paid for by the many to benefit the few."
The Tories said Labour were "in denial about the reality of access to GPs".
Andrew Lansley, their health spokesman, said: "Patients find it increasingly difficult to get an appointment within the 48-hour target time and are unable to make a forward appointment.
"It is Labour's targets that have let down patients and GPs."