They will be tried at Coventry Magistrates' Court on 5 and 6 November.
An Insolvency Service spokesman confirmed that "criminal proceedings have been commenced against David Smith, Robert Peto and Thomas Wright".
"We will not be commenting until the criminal proceedings have been concluded," they added.
The Insolvency Service said that the Department for Business, Innovation and Skills (BIS) was bringing the prosecution on its behalf.
Coventry-based City Link, owned by investment firm Better Capital, called in administrators on Christmas Eve after "substantial losses".
On New Year's Eve it announced 2,356 job losses after a bid to buy the company failed.  A week later it announced a further 230 redundancies.
The company was founded in 1969. It was bought by Better Capital for Â£1 in April 2013.
Ex-directors of failed parcel firm City Link are being prosecuted under section 194 of the Trade Union and Labour Relations (Consolidation) Act 1992.