A spokesman for Keenes, which was acquired by Australian pre-press group Wellcom for £4.2m in September 2007, confirmed Keene's departure.
The company said that Keene was currently on gardening leave. Jeff Keene declined to comment on his departure.
Following Keene's departure there will no longer be a Keene family member employed at the business, which was family-owned prior to its sale to Wellcom.
Keenes general manager Barrie Lambert said that the company would continue to operate under its existing four-man management team, without a managing director.
"Australian companies don't typically have managing directors, so we've had a management restructure and the existing management team will now be responsible for taking the business forward," he added.
In addition to Lambert, the management team includes creative services director Chris Grawe, production director Andy Gladden and financial director Colin Kirk.
Keenes was sold to Wellcom in a £4.2m deal, which completed on 1 October 2007. It is understood that former chief executive Fred Keene left the business a short time after the sale.
Keenes employs around 70 people and has an annual turnover of £5m, with a client roster that includes Mills & Boon, GAP Inc, Sony, HSBC, Harrods and DKNY.