Queensland and Victoria believe they have wound up with less federal funding for hospitals than they are owed for 2016-17.
But the federal government says its public hospital funding has been based on the advice of two independent umpires.
Treasurer Josh Frydenberg on Friday signed off on a final top up payment of $307 million for the states and territories for hospitals in the last financial year, which follows a $354 million boost in June.
That brings the commonwealth's total hospital funding to $19 billion in 2016-17, which is $1.6 billion more than it spent the year before.
The latest top ups are aimed at ensuring the states and territories get what they are entitled to, based on calculations by the Independent Hospital Pricing Authority and administrator of the National Health Funding Body.
Prime Minister Scott Morrison says the health funding formulas are "straightforward".
"There are reconciliations done on those from year to year and we're just following the normal process," he told reporters on Monday.
But Queensland and Victoria say the funding they are getting is less than they deserve, due to statistical adjustments that have come after services have been delivered.
Queensland Health, which was expecting $79 million more than the $4.1 billion it received, says it will continue to oppose such revisions.
"Such retrospective adjustments after the activity has already been delivered flow into funding for subsequent years and make it very difficult to plan service delivery," the department told AAP.
Victorian Health Minister Jill Hennessy said the federal government was cutting $201 million from Victoria's hospitals for services they have already provided.
"Scott Morrison is trying to cover up yet another round of brutal cuts to Victoria's hospitals. Whether it's Abbott, Turnbull or Morrison, the cuts remain the same," Ms Hennessy told AAP in a statement.
But Health Minister Greg Hunt says the amounts paid were recommended by the two authorities chosen by the states.
"The commonwealth is happy to accept the decision of the independent umpires," Mr Hunt said in a statement.
The pushback comes as the federal government is urging Victoria and Queensland to sign up to a new national hospital funding agreement, due to start in mid-2020.
It has earnt the backing of the other states and territories.
Mr Hunt is due to meet with his state and territory colleagues on October 12.
