More than three tonnes of the white powder was stored in containers.
Chaos broke out in Port Moresby as opportunists looted stores while the country's police held a protest.
The boat overturned near Tuvuca Island, Fiji Police said in a statement.
The quake was at a depth of 10km.
“Because nothing is going out to the communities telling them to protect themselves, people are going back to doing the risky behaviour.”
"Mal should fall apart north of New Zealand," said WeatherWatch forecaster Philip Duncan.
Mal is expected to pass close to the west of Fiji on Tuesday evening.
Police are urging the public not to attempt to cross any flooded roads.
He walked out of the forum on Thursday.