The suspects, aged between 30 and 63, were detained in raids across Singapore on Sunday after the Anglo-Dutch energy giant first alerted police in August. Several of the suspects were Shell employees.
A total of Sg$3.05 million ($2.3 million) in cash was recovered along with a 12,000-tonne tanker, which police believe was where the stolen oil was being transferred.
The suspects' bank accounts have also been frozen, police added.
Authorities charged 11 of the men in court on Tuesday, including eight Singaporean employees of Shell and two Vietnamese men -- a crew member and the captain from the oil tanker Prime South.
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The 11th suspect was a Singaporean who did not work for Shell. The other six are still under investigation.
The oil was allegedly stolen from the Pulau Bukom industrial site in western Singapore, which Shell describes as one of its most important production centres in the world.
The fuel was taken on at least three occasions, according to court documents seen by AFP.
On November 21, five Shell employees were alleged to have taken fuel worth nearly Sg$1.28 million.
Meanwhile, a further three Shell employees were alleged to have taken Sg$438,000 worth of fuel on January 5.
On Sunday, four of the Shell workers together with a fifth man not employed by the oil giant, were alleged to have stolen fuel worth Sg$688,000.
The two Vietnamese crew of the Prime South have been charged with "dishonestly receiving stolen property".
No plea was taken and the men will appear in court again later this month.
Shell said in a statement the company anticipates a "short delay in the supply operations at Bukom, but at this point we expect to continue to meet our contractual supply obligations to customers".
Singapore is one of the world's largest oil trading hubs with huge quantities of crude from the Middle East passing through the city-state before going on to East Asia, and several oil majors have local refineries.