The 32-year-old Portuguese star is holidaying in the Balearic Islands along with his girlfriend Georgina Rodriguez and family, according to Spain's Hola celebrity magazine, which first reported the story.
The magazine published photos of three uniformed customs agents arriving on a motorised rubber dinghy before boarding the grey yacht where an awning was pulled down over the main part of the boat as they went about their inspection.
News of the inspection, which took place on Tuesday, made waves -- coming as it does just three weeks before Ronaldo appears before a judge, accused of evading 14.7 million euros ($16.8 million) in taxes.
But a source at Spain's tax agency, who refused to be named, said it was merely "a routine check of vessels."
"We do this every summer in the Balearic Islands. It doesn't affect those who use the boats, it's related to charter companies' registration taxes."