Australians will continue to receive cheaper medicines, but a push to scrap the policy could be brought back to parliament if pharmacists' concerns are ignored.
Under Labor's plan, which started on September 1, consumers with chronic conditions are able to get two months' worth of medicine for the price of one.
The initial list of medicines includes treatments for people with a heart condition, Crohn's disease, high cholesterol, osteoporosis, high blood pressure and many other conditions.
But pharmacists, who gathered outside Parliament House in Canberra on Monday at the start of a fortnight of sittings, say the measure threatens their financial viability.
The government last week offered an olive branch by bringing forward community pharmacy agreement negotiations by more than a year.
The agreements usually last five years and spell out how much pharmacies are reimbursed by the government for dispensing drugs listed on the Pharmaceutical Benefits Scheme.
Prime Minister Anthony Albanese was interrupted in question time by dozens of Pharmacy Guild members in the public gallery, who began coughing when the medicine changes were mentioned.
The outburst prompted a stern rebuke from Speaker Milton Dick.
"I remind all visitors today there are established forms of behaviour. You are here to observe, and not participate," he said.
Mr Albanese said the government was working alongside community pharmacies on the changes.
Health Minister Mark Butler said community pharmacies had been consulted on the changes, saying the opposition had ignored the needs of patients.
"The measures that we delivered on Friday ... deliver cheaper medicines for almost four million Australian patients," he told parliament on Monday.
"I've been asked question after question by (the opposition) about this measure."
The federal opposition was due to move a disallowance motion in the Senate which would have overturned the new policy.
But opposition health spokeswoman Anne Ruston said she would no longer proceed with it after the government agreed to bring forward the agreement talks.
However, Senator Ruston warned the motion could be brought back on if the government did not show good faith in addressing concerns from pharmacists about lost revenue and other impacts.
Nationals leader David Littleproud said the policy change would have a profound impact in rural and regional communities which don't have thousands of customers to offset the revenue hit.
"Those that have just gone in and borrowed on a business model from their bank saying, 'I'll get $8 every time I dispense a medicine and this is the number of medicines in this community', their business model is gone and their banks are asking questions," he said.
Mr Littleproud claimed the new agreement timeline as a win, saying it was an admission by the government they had got the balance wrong.
Mr Butler said whole he had not put a date on negotiations for the next pharmacy agreement, but indicated the Pharmacy Guild had sought for it to be signed off by March next year.
The minister has said the changes would only have a modest impact on the sector's bottom line with a one to two per cent hit.
Growth of 30 per cent over the past four years provided a buffer, he said.
Mr Butler has also been critical of the pharmacy lobby for standing in the way of cheaper medicines to relieve the cost of living.