The move would leave practices facing fines of up to 10% of their turnover if they breach licensing conditions concerning competition and pricing.
GPs could also be forced to pay for licences, on top of CQC registration fees that could hit £1,600 for some practices in the coming years.
Monitor senior policy adviser Paul Dinkin, the man heading its primary care consultation, said his initial conclusion was that Monitor would play a major part in primary care.
The BMA and the RCGP have opposed licensing. The college has warned about promoting competition for its own sake against the interests of patients and local health economies.
After a consultation on licensing in March, the DH said primary care providers would be exempt pending a review in 2016/17. But at a conference for GP out-of-hours group Urgent Health UK, Mr Dinkin said: 'We expect that over time, primary care providers will probably come into the fold and require licences'.
GPC deputy chairman Dr Richard Vautrey said the latest comments from Monitor were a sign of the fragmented and costly bureaucracy GP practices were subject to.
'We made the case that there was no value or need for practices to be licensed and regulated by CQC and Monitor in addition to being performance managed by NHS England,' he said. 'I don't believe anything has changed to alter that position.'
Mr Dinkin said that to obtain a licence, 'you just have to be CQC registered'. He added: 'But once you've got it, we've got the enforcement bit, to say to you, you're misbehaving.'
Mr Dinkin said his review was looking at barriers to entry into general practice, such as practice boundaries and registered lists.
'They're there to preserve one of two things: demand management and continuity of care. The sorts of questions we ask as regulator are: are there other ways of meeting those objectives that allow a bit more flexibility to come into the market?'
He said the BMA and the RCGP were wrong to say general practice needed more funding. 'Our suspicion is not more money for the current model, but to rethink who does what.'