BBC Worldwide paid a nominal fee of £100 for 10,000 shares in Bedder 6, which was set up by Clarkson and 'Top Gear' executive producer Andy Wilman in 2006 for unknown reasons.
Some but not all of 'Top Gear's' commercial revenue will be funnelled through the company. It is expected to receive profits for 'Top Gear' merchandising and some of the commercial activities relating to the show, including foreign sales of the original UK production.
A spokesperson for BBC Worldwide said: "In relation to the company, BBC Worldwide decided to enter into a commercial arrangement to better exploit the commercial potential of 'Top Gear', predominantly internationally.
"This benefits the licence-fee payer in the long run and means increased revenues are being invested back into programme making."
Clarkson and Wilman own 3,000 and 2,000 shares respectively and will be entitled to a share of the money from some of 'Top Gear's' revenues.
BBC Worldwide's West London headquarters became the registered office for Bedder 6 in November 2007 and three of its executives were made directors of the company.
The deal may have persuaded Clarkson, who was rumoured to be planning to defect to ITV unless he received a greater share of profits from the programme, to stay with the BBC.
Earlier this month, presenters Richard Hammond and James May verbally agreed a new deal with the BBC to stay with the programme.
BBC Worldwide has been expanding the 'Top Gear' brand in the UK and globally over the last 18 months.
It has been licensed to more than 40 international broadcasters and filming began for a US pilot version of the show in June, fronted by outspoken Los Angeles comedian Adam Carrola.
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