Shell's Bukom refinery is its biggest plant worldwide and makes up more than a third of Singapore's capacity. The company faces a fine of up to S$500,000 (£253,000) if convicted in the case, which is to be heard by a court on 25 September.
Singapore's Ministry of Manpower filed a charge against Shell on 31 August for an offence under the Workplace Safety and Health Act for the lapses in safety, the ministry said in a statement late last night.
Shell declined comment on the matter as the case is before the courts.
"We have extended our full cooperation to the relevant authorities," a spokeswoman said this morning. "Safety is a top priority for Shell. We regret this incident and are applying the lessons to avoid such an occurrence in the future."
Last September, Shell shut its Bukom refinery for just over two weeks after the fire forced the oil major to declare a force majeure on sales of some oil products and on some crude purchases. This is a condition in contracts that exempts buyers or sellers from commitments in case of events that are beyond control.