There have been no reports of an oil spill or disruption to shipping traffic in the Singapore Strait, it said.
According to the MPA, the dredger capsized as a result of the accident and is now partially submerged. Of the 12 crew members on board, the seven injured were rescued by the police coast guard and taken to Singapore General Hospital at 2.45am. In a sea launched a search-and-rescue mission for help were sent to court and a helicopter.
The incident took place in the westbound lane in the Singapore Strait, where the dredger was transiting and the Indonesian-registered tanker Kartika Segara was leaving Singapore to join the eastbound lane.
The capsized vessel was moved to a safe area near Pulau Senang with the help of two Singaporean tug boats.
The collision was between an Indonesian-registered tanker carrying 26 crew members from the country and a Dominican-registered dredger carrying 11 crew members of Chinese and one of Malaysian origin.
The MPA also said that vessel traffic control had given warnings to both vessels prior to the collision.
Five crew members were reported missing after a tanker and a boat collided in Singapore waters at about 12:40 am, said the Maritime and Port Authority (MPA).
Search and rescue efforts, led by the MPA, for the remaining three crew members are ongoing. The MPA has told ships to look out for the missing crew and to navigate with caution near the collision site.
The shipping lanes around Singapore are among the world's busiest and its navigational challenges include a narrow strait, frequently limited visibility and thousands of vessels sailing through daily.
The agency is now investigating the cause of the incident.
Wednesday morning's collision follows the one on August 21, when the United States warship USS John S. McCain collided with a merchant vessel in Singapore territorial waters near Pedra Branca.