She was arrested in Fivemiletown last month after the firm told police it had concerns about its accounts.
The 41-year-old is accused of fraud by abuse of position, concealing criminal property and making, having and supplying articles for use in fraud.
She will appear at Dungannon Magistrates' Court on 1 July.
A woman has been charged for a fraud at a County Tyrone manufacturing company that is understood to run into the millions of pounds.