The three victims, all from Myanmar, raised the number of confirmed deaths in the blasts to five. Three more workers were still listed as missing as of press time on Wednesday.
The Smooth Sea 22 tanker arrived at the dockyard for maintenance on January 12 and informed dockyard authorities that it was still carrying residual bunker oil and diesel oil.
It exploded during welding work at about 9am on Tuesday.
Those killed and injured in the blasts were all dockworkers.
All 17 crew members from the tanker are safe and accounted for.
The three missing workers were identified as Wichian Boonlert, a Thai national, and two Myanmar workers named only as Zoul and Tila.
Rescuers found two victims, one Myanmar worker and one unidentified, from the explosions on Tuesday before resuming their search on Wednesday.
Bodies of three Myanmar workers were retrieved from the water between 9am and 11am on Wednesday. The victims were named as Winbo, Dungae and Sawmin. Myanmar nationals often go by only one name.
Cholthee Laohakamwanit, head of the rescue operation, said rescuers had searched the hull of the tanker but found no survivors or bodies inside. Scuba divers joined the search on Wednesday, he added.
Samut Songkram governor Somnuek Promkhiew has ordered the Tambon Ban Khiew Administrative Organisation to set up a command centre to coordinate the search operation and to receive complaints from locals whose houses were damaged by the blast.
Samran said he was sitting in his living room when he heard two huge explosions that brought down his ceiling and shattered the window.
Wasukree said he lost his one-year-old American Bulldog to the blasts, which also shattered his windows, cracked his walls and brought down ceiling lights.