A senior Australian intelligence chief has acknowledged a landmark climate and security deal with Tuvalu may be at risk in the wake of the Pacific nation’s election.

Andrew Shearer, who leads the government’s Office of National Intelligence (ONI), said his agency was “obviously aware of recent political change and turbulence in Tuvalu”.

But he cautioned that he could not yet predict the fate of the deal because ONI was not part of the negotiations between the two countries.

The treaty, signed in November, offered “a special human mobility pathway for citizens of Tuvalu” to live, study and work in Australia as part of recognition that the low-lying Pacific country was particularly vulnerable to sea level rise.

Just as significantly, the treaty promises that Australia will defend Tuvalu in the case of any military aggression or other significant threats.

In return for this security guarantee, Tuvalu must “mutually agree with Australia” if it wants to strike a deal with any other country on security and defence-related matters.

This measure was widely been seen as an effective Australian veto on a potential future security agreement with China. Tuvalu currently is one of the few nations to maintain diplomatic relations with Taiwan, not Beijing.

But at a Senate estimates hearing on Monday night, the Greens senator David Shoebridge noted that the prime minister who signed the deal with Australia, Kausea Natano, had lost his seat in elections held late last month.

There are no political parties in Tuvalu’s parliament, where two lawmakers are elected in each of eight island electorates, and the formation of the new government may take some time.

Shoebridge asked Shearer whether it was his assessment that the agreement with Tuvalu “faces a real risk of unravelling now”.

Shearer replied: “My assessment, Senator, would be that we are obviously aware of recent political change and turbulence in Tuvalu. But we’re not a party to the negotiations between the Australian government.”

Shoebridge retorted: “It’s an election, they elected somebody who campaigned against the deal cut with Australia. That’s not turbulence. That’s democracy.”

Shoebridge added that despite the “grand trumpeting” of the deal last year, “it looks like it’s all going to fall over because the people of Tuvalu just had an election and said, ‘No, thanks’”.

Shearer, in an implicit acknowledgment that the deal was now in doubt, replied: “My understanding is that the current position of the government of Tuvalu is along the lines that you articulated.”

The Coalition’s foreign affairs spokesperson, Simon Birmingham, said he believed there were “genuine risks and questions to be asked about how the agreement will likely be handled”.

“My understanding is that Tuvalu has not yet formed a new government following the elections,” Birmingham said.

“The composition of the parliament has clearly changed, but it is not yet at the point that the new government has actually been formed, as I understand.”

The Tuvalu-Australia agreement was raised during a Senate estimates hearing amid discussion of ONI’s climate security risk assessment, which remains under wraps.

Shearer said climate change was “one of our highest analytical priorities” and it had “deep and complex relationships with other security threats that we’re facing”.

He said that meant it was not possible to rank the climate crisis against other security threats in a “stark” manner. He agreed that the climate crisis was “one of the most significant security risks Australia faces”.

The assistant minister for trade, Tim Ayres, said the government had heard calls for a version of the ONI report to be released to the public, but continued to hold the position “that security advice provided by the office is not released”.

Ayres said the report “informs the government’s judgments” about climate change.

He said the deal with Tuvalu was “an example of a measure that the Australian government has undertaken with one of the Pacific nations that goes squarely towards these issues”.

Shearer also used his appearance before the committee to warn that “Australia’s international environment has become only more complicated” in recent months.

He said ONI and the broader national intelligence community were “working hard to help the government make sense of a dynamic and very complex operating environment for Australia”.

“The attack by Hamas on Israel on 7 October last year, the conflict in Gaza and spillover into the Red Sea, Syria and Iraq and the uptick in fighting along the Israel-Lebanon border, have been a major focus,” Shearer said.

“The risk of further escalation in the Middle East remains very real. This comes on top of existing priorities, including the grinding war in Ukraine.”

Shearer raised concern about “more extensive and consequential strategic cooperation between authoritarian revisionist powers, such as North Korea’s provision of ballistic missiles and ammunition to Russia, and Iran’s supply of armed drones” to Houthi rebels in Yemen.