The proposals will force health boards to inform affected practices and consult the local community when processing pharmacy applications.
Health boards must also consult a representative of the area medical committee and companies will have to wait 12 months before reapplying after an application is turned down.
Dr Andrew Buist, deputy chairman of GPC Scotland, welcomed the proposals but said they had come too late for many practices in Scotland.
'We think these proposals are right but it would be good if they had been introduced 18 months ago.
'There has been a window of opportunity for pharmacy applications recently and many of the easy pickings have been picked, and many practices have lost their right to dispense.'
Dr Buist said the new pharmacy contract had made many of Scotland's rural communities more attractive to pharmacies.
But the changes make the application process 'more robust,' said Dr Buist, which would end speculative applications.
'It should help avoid the situation where practices worry that, despite an application being turned down, the pharmacy will apply again literally a couple of weeks later,' he said.
Giving the community a voice in the application process was also positive, he said.
Dr David Bailey, the GPC's dispensing lead, said the rest of the UK's pharmacy applications process was already more robust than Scotland's.
But the GPC is hoping that the dispensing contract can be renegotiated following a DoH enquiry.
The government has commissioned a 'cost of service' inquiry into the funding of dispensing services which is due to report soon.
'The process of application is more robust in England and Wales and we wouldn't want to see them change again,' said Dr Bailey.
'But we will certainly want to talk about the inquiry and whether the dispensing contract should be renegotiated.'