A withering audit of the 2010 deal struck between the federal government and the Pharmacy Guild found it lacked transparency and was messy in its implementation.

The fifth Community Pharmacy Agreement committed the government to paying $15.4 billion to the Pharmacy Guild to dispense medicines listed under the Pharmaceutical Benefits Scheme to the public over five years.

The Australian National Audit Office reported in March that there were "shortcomings in key aspects of Health's administration at the development, negotiation and implementation phases" of the agreement.

These included the department's failure to keep official records of its negotiations with Pharmacy Guild officials, which was "not consistent with sound practice", and its re-allocation of money between programs after the contract had been signed, without ministerial approval.

Far from the agreement delivering $1 billion in expected savings as intended, the auditor's analysis found net savings would be closer to $400 million.

The Department of Health has now confirmed that no action has been taken against any staff in response to the report in an answer given to questions taken on notice at budget estimates.

It accepted that it was "better practice" to prepare official records of meetings.

"Nevertheless, it should not be inferred that the department is not in possession of any records in relation to these meetings," the department said.

"Sufficient records were kept to ensure that the matters agreed during the negotiations were encapsulated in successive versions of the draft agreement and ultimately in the 5CPA itself."

In June, the government signed off on the sixth Community Pharmacy Agreement, which includes a tender process for government-funded programs previously administered by the guild.

But Greens senator Richard Di Natale said that in signing the $19 billion agreement, the government did not address any of the transparency issues identified by the auditor in relation to its predecessor.

"We can't evaluate or assess whether we're getting any value for this money," Senator Di Natale said.

"It's still a negotiation between two parties that's very opaque. We should know at least the terms and conditions on which the agreement is based.

"The worst thing about it is they get away with it. The audit office report comes in damning and the whole caravan moves on."

The audit report quantified for the first time that the amount paid by the government to pharmacies has tripled in real terms since 1990.

University of Melbourne health economist Philip Clarke said these statistics should be made routinely available to provide accountability to taxpayers and assess claims by the industry that particular government policies would send them out of business.

"There needs to be greater transparency and reporting around the remuneration pharmacists get for Community Pharmacy Agreements over time," Professor Clarke said.