Royal Caribbean Cruises has cancelled a planned call to San Juan, Puerto Rico, amid political strife in the US territory's capital city.

Thousands of protesters on Monday marched the city's streets, calling for governor Ricardo Rossello to step down two days after the reported discovery of inappropriate emails with closest aides.

"In light of current unrest in San Juan, Puerto Rico, we have canceled today’s call to San Juan," Royal Caribbean spokesman Owen Torres said in a statement to USA Today.

"We continue to monitor the situation closely and will make adjustments as necessary to ensure the safety and security of our guests and crew."

An email to Torres was not immediately returned.

Royal Caribbean's 48,600-gt Empress of the Seas (built 1990) skipped its San Juan stop Tuesday and moved on to its next scheduled call to British Virgin Islands' Tortola, Torres said

Guests will be fully refunded for prepaid shore excursions in San Juan, he told USA Today.

Torres said Richard Fain-led Royal Caribbean has not cancelled future calls to San Juan but is "monitoring the situation and will make adjustments if necessary."