Joe Biden has moved to repair his damaged personal and political relationship with Emmanuel Macron by acknowledging that the announcement of a security and technology pact that blindsided France was a “clumsy” episode handled with a lack of grace.

The US president and his French counterpart met at France’s Vatican embassy in Rome on Friday, ahead of the G20 leaders’ summit this weekend, for their first in-person discussion since an astonished Macron was left feeling betrayed and humiliated by September’s security deal.

As a result of the “Aukus” pact between the US, Australia and the UK, Australia tore up a troubled $66bn (GBP48bn) contract signed with France to build six diesel-powered submarines in favour of a deal with the US for eight nuclear-powered submarines. It was the first time the US had offered to share its nuclear technology with a third party other than the UK.

Sitting next to Macron before a bilateral meeting, Biden also implied that he thought Australia had already informed France that it was cancelling its submarine contract.

“The answer is – I think what happened was to use an English phrase … clumsy, it was not done with a lot of grace,” Biden said.

“I was under the impression that France had been informed long before, that the [French] deal was not going through,” he said, which suggests either his staff failed to inform him, or Australia misled the White House about what it had told the French.

There is no suggestion from the White House that Macron himself knew the contract had been cancelled, a point that the French have shown in published exchanges with the Australians days before the contract was cancelled.

The two leaders met for nearly an hour and a half at the Villa Bonaparte, the French embassy to the Vatican. A senior US official said that for more than half that time, Macron and Biden were alone.

“It was a very meaty, substantive but I would say broad-ranging and strategic conversation,” a senior US official said, adding that the leaders spent a “fair amount of time talking about the challenge posed by the rise of China.”

“I don’t worry at all about instability or drift in the US-France relationship,” the official added, saying relations had been given a “jolt of energy” in the past month. “We had some hard conversations in September and October, I think the conversations heading into November will be exciting and engaging. There’s not any sense that there’s some kind of fundamental rift in the relationship.”

The two leaders issued an unusually long joint statement after the meeting, highlighting areas of agreement. Biden pledged to step up US support for French-led counter-terrorist operations in the Sahel. The two leaders welcomed the establishment of a bilateral clean energy partnership by the end of the year, they affirmed their faith in Nato and its nuclear deterrent capability, and “robust” collaboration in the Indo-Pacific.

Biden called France an “extremely, extremely valued partner … and a power in itself” with the “same values” as the US. Macron said the meeting was the start of a process of rebuilding trust but said concrete decisions had already been taken to develop cooperation.

The secretive handling of the submarine deal, and the effective elbowing out of France from the Indo-Pacific, was in part driven by a US belief that France did not support a real confrontation with China.

But the handling of the episode led to soul-searching in Washington, and an acceptance it needed to do more than make gestures of reconciliation to Macron.

France regards the new agreement as necessary diplomatic and security recompense, and a successful effort to retrieve something positive from the debris of the cancelled Australian contract, which shook French trust in the Biden administration, symbolised by the temporary recall of the French ambassadors to Washington and Canberra.

Macron, in common with past French presidents, has long championed a stronger, separate European defence identity that he says can be complementary and not duplicatory of Nato. But he has faced resistance from Germany, and some Nordic EU states that fear EU defence will mean losing the protection of the US within Nato.

An implicit Biden endorsement of the Macron project may help ease some of the objections inside the EU, as well as play well for a US domestic audience keen to reduce the global US military footprint. Macron will develop the theme of a more autonomous European defence project as part of the six month French presidency starting in January.

Biden sees the shift as part of an effort to focus US military resources on competing with the growing military strength of China in the Indo-Pacific.

Before the meeting an Elysee source said it “will be an occasion to show that after the Aukus affair, we have been able to jointly negotiate significant elements of cooperation on key communal issues”.

The Elysee said the meeting set a clear framework for the future French-US relationship and “set a very high level of ambition for relations between the EU and the US, with a strong emphasis on security and defence”.

The Elysee said a key topic would be “our common security” namely European defence and transatlantic defence ties. Macron’s office stressed that there was “no contradiction between European defence and the Atlantic alliance”.

The Macron-Biden reconciliation, prepared in intensive talks over the last month, will help to heal some but not all of France’s wounds, but still leaves untreated soured relations between France and Australia, including the issue of compensation to France for cancellation of the contract.

France’s relations with Britain are deteriorating separately across a range of largely Brexit- rather than security-related issues.

The Aukus agreement is also facing growing questions in Australia, with some politicians asking why Canberra has abandoned the certainty of purchasing French diesel-powered engines to become involved in buying nuclear-powered submarines that will be subject to an 18-month scoping study followed by a delay of decades.