MANILA, Philippines — The Philippines accused China on Tuesday of intimidating its fishermen at a disputed South China Sea shoal, and normalizing an “illegal presence,” after Beijing sent its largest coast guard vessel into Manila’s maritime zone.

The move comes against the backdrop of rising tension between the Philippines, a U.S. treaty ally, and Beijing during the past two years, stemming from their overlapping claims in the busy waterway of the South China Sea.

The Philippines has…