WATCH: Rubio says Trump prefers Cuba diplomatic solution, but says likelihood 'is not high'

Secretary of State Marco Rubio said Thursday that the Trump administration is keen to find a diplomatic solution to its differences with the Cuban government, but is not particularly optimistic that one can be achieved.

Watch Rubio's full remarks to reporters in the video player above.

His comments leave open the option of military action against Cuba, particularly after the indictment this week of former President Raúl Castro on terrorism charges.

WATCH: Blanche says he expects Raúl Castro to face charges in U.S. of his own will 'or another way'

"The president's preference is always a negotiated agreement that's peaceful," Rubio told reporters before leaving Miami for a trip to Sweden and India. "That's always our preference. That remains our preference with Cuba. 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 added that "our preference in Cuba and anywhere in the world is a negotiated diplomatic settlement."

Rubio says Cuba has 'always' been a national security threat

The U.S. secretary of state says Cuba has "always" been a national security threat to the United States.

"Cuba hosts a Russia and Chinese intelligence presence in their country," Rubio told reporters before leaving Miami for a trip to a NATO foreign ministers meeting in Sweden and then India.

WATCH: Trump says Raúl Castro indictment is 'a very important moment' for Cubans

Rubio would not discuss how the U.S. might move to implement the indictment against Castro, which has led many to believe that military action against the island is potentially imminent, after similar charges against former Venezuelan leader Nicolas Maduro were invoked to justify his ouster in a military operation in January.

Rubio says Iran's plan to toll Strait of Hormuz would make deal 'unfeasible'

Rubio once again blasted Tehran's effort to financially benefit from its chokehold on the critical waterway.

"No one in the world is in favor of a tolling system. It can't happen. It would be unacceptable," he said. "It would make a diplomatic deal unfeasible if they were to continue to pursue that."

But the secretary of state added that there were "good signs" in the ongoing negotiations between the U.S. and Iran despite weeks of back-and-forth on a sustainable end to the war between the longtime adversaries.

"I don't want to get ahead of it ... I think we've made some progress," Rubio said. "But obviously we're dealing with a system that itself is a little fractured."

Rubio says despite 'good signs' in Iran talks, 'other options' remain on the table

Being careful not to sound overtly optimistic, Rubio said that while Pakistan and other regional allies are hard at work to bring a diplomatic resolution on Iran, with some officials traveling to Tehran today, Washington remains ready with alternative plans.

"The president's preference is to do a good deal. That's his preference. It's always been his preference. If we can get a good deal done, that would be great," he said. "But if we can't get a good deal, the president's been clear he has other options."