The US president, Donald Trump, and the secretary of state, Marco Rubio, on Thursday again raised the spectre of military intervention in Cuba, a renewed threat that takes on greater weight a day after the administration announced criminal charges against Raúl Castro, the island’s former leader.

“Other presidents have looked at this for 50, 60 years, doing something,” Trump told reporters when asked about Cuba during an event in the Oval Office. “And it looks like I’ll be the one that does it. So I would be happy to do it.”

Rubio told reporters separately that Cuba had been a national security threat for years because of its ties to US adversaries and that Trump was intent on addressing it.

Rubio, the son of Cuban immigrants who has long taken a hard line against the country’s socialist leadership, said the Trump administration wanted to resolve differences with Havana peacefully but was doubtful the US could reach a diplomatic resolution with the island’s current government.

“[Trump’s] preference is always a negotiated agreement that’s peaceful. That’s always our preference. That remains our preference with Cuba,” Rubio said in Miami before boarding a plane to attend a Nato meeting in Sweden and visiting India. “I’m just being honest with you, you know, the likelihood of that happening, given who we’re dealing with right now, is not high,” he said.

Several of Trump’s senior aides – including Rubio, the CIA chief, John Ratcliffe, and other senior national security officials – have met Cuban officials in recent months in an effort to improve relations. But US officials reportedly came away dissatisfied, prompting a fresh wave of sanctions against the Cuban government over the past week.

Over the years, Cuba had become accustomed to “buying time and waiting us out,” Rubio said. “They’re not going to be able to wait us out or buy time. We’re very serious, we’re very focused.”

When asked whether the US would use force to change Cuba’s political system, Rubio repeated that a diplomatic settlement was preferred but noted that “the president always has the option to do whatever it takes to support and protect the national interest”.

He dismissed a reporter’s suggestion that the move resembled “nation-building”, insisting it was instead aimed at addressing a national security threat.

On Wednesday, federal prosecutors announced an indictment that accuses Castro of ordering the shooting down of civilian planes flown by Miami-based exiles in 1996. The charges, filed in secret by a grand jury in April, include murder and destruction of an aircraft.

The Cuban president, Miguel Díaz-Canel, condemned the indictment as a political stunt designed to “justify the folly of a military aggression against Cuba”.

The Castro indictment has fuelled speculation that the Trump administration is following the same playbook it used before the operation in January that led to the capture of the Venezuelan president Nicolás Maduro, who was charged with drug trafficking, has pleaded not guilty and remains imprisoned in the US.

The US military also highlighted the arrival of the USS Nimitz aircraft carrier and accompanying ships to the Caribbean Sea on the same day the charges against Castro were announced. US Southern Command said the vessels were participating in maritime exercises with partners in Latin America that began in March.

Rubio declined to discuss how the US might seek to enforce the indictment against Castro, who turns 95 next month.

Trump has threatened military action in Cuba since ousting Maduro and ordering an energy blockade that choked off fuel shipments to the country. This has led to severe blackouts, food shortages and economic collapse on the island.

This month, the Trump administration also imposed new sanctions on Cuba, the largest of which is against Grupo de Administración Empresarial SA (Gaesa), a business conglomerate operated by the Cuban Revolutionary Armed Forces.

On Thursday, Rubio announced that the sister of Gaesa’s executive president, who was living in the US, had her green card revoked and was taken into ICE custody.

Rubio said: “Past administrations have permitted the families of Cuban military elites, Iranian terrorists and other reprehensible organisations to enjoy lavish lifestyles in our country funded by stolen blood-money, while the people they repress at home suffer in increasingly dire circumstances. No longer.”

Trump has also escalated speculation of regime change in Cuba, pledging a “friendly takeover” if the country’s leadership did not open its economy to American investment and expel US adversaries.

Rubio said Cuba posed a serious national security threat to the US because of its security and intelligence ties with China and Russia as well as its friendly relations with US adversaries in Latin America.

China condemned US sanctions and pressure on Cuba. A foreign ministry spokesperson, Guo Jiakun, said: “China firmly supports Cuba in safeguarding its national sovereignty and national dignity and opposes external interference.”