Leaders in Papua New Guinea and Vanuatu have raised issues with the proposed security agreements, which had appeared all but finalised, putting their approval in question.
Both pacts are aimed at shoring up Australia's position as a first-choice security partner for Pacific neighbours, who are also being courted by China.
Vanuatu Prime Minister Ishmael Kalsakau on Tuesday said some in his nation believed a pact agreed last year, but not yet ratified, could give the Australian military too much power.
"We must remove the stigma that the agreement is one-sided and does not reflect Vanuatu's sovereignty," he said.
"Thinking that some troops from Australia will enter the country without visas and access our sovereign data will not happen, unless we agree and give our informed consent."
His comments came after Papua New Guinea rejected a draft defence treaty, with Prime Minister James Marape saying that certain, unspecified provisions encroached on his country's "sovereign rights".
He said Australian officials had been asked to re-work the draft, describing it as a work in progress.
Papua New Guinea officials have described the issues as "highly confidential".
In May, Papua New Guinea signed a defence pact with the United States, sparking student protests and calls for more transparency.
Many Pacific nations are still coming to grips with the legacy of a colonial past, as they navigate increased competition between China and Western countries.
Canberra was caught off-guard when China and Solomon Islands signed a secretive security pact in April last year, and has been scrambling to reinforce its relationships with Pacific neighbours ever since.
The South Pacific is home to shipping lanes and ocean resources and could become a crucial military theatre in the event of a war over Taiwan.
Australian Defence Minister Richard Marles on Tuesday met with Kalsakau in Vanuatu's capital Port Vila, where he played down suggestions the agreement could be derailed.
"It's going to be a really important agreement between our two countries," he told reporters.
"We're very happy with the progress that is being made here in Vanuatu in relation to it and the progress that's also been made in Australia."
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