The pilot fell overboard while disembarking from a tugboat to board a launch boat off the Southern Islands, said the Maritime and Port Authority of Singapore (MPA), adding that he was wearing a lifejacket at the time.
The authority's marine safety control centre was alerted to the incident at about 2.50am.
MPA, the Police Coast Guard and the Singapore Civil Defence Force (SCDF) deployed patrol and emergency response vessels to conduct search and rescue operations.
"MPA also activated divers to conduct an underwater search for the missing pilot and issued navigational safety broadcasts to the surrounding vessels to support the search efforts," the agency added.
A harbour pilot's work involves boarding vessels to navigate them through congested waters.
In response to CNA's queries, SCDF and the police said the incident took place near Kusu Island, which is part of the Southern Islands.
SCDF added that it deployed two marine vessels and conducted a surface search at the location.
The pilot's body was recovered at about 11.30am and taken to the Police Coast Guard base on Pulau Brani.
MPA said investigations are ongoing.
CNA has contacted the Ministry of Manpower and PSA Marine for more information.