Simon Jones, 41, was dismissed last week from his position as commercial manager of National Trust Enterprises Ltd in Westbury, Wiltshire. It produces and markets items such as kitchen towels and food for sale on behalf of the trust.
The organisation has a pounds 37m annual turnover and makes about pounds 7m a year profit for the trust. The sum of money alleged to be involved is in the region of pounds 50,000.
Mr Jones was arrested by Wiltshire detectives who had been called in by National Trust Enterprises. After being interviewed by police, he was released on bail. Sources said the investigation involved the alleged channelling of funds into private accounts.
Mr Jones was the third most senior manager of the organisation, answerable to Anne Roberts, the managing director, and her deputy, and was in charge of all its financial activities.
The organisation, which has a headquarters staff of around 30, is separate from the National Trust proper which, as a charity, is unable to market products. A spokeswoman for the trust said: 'A member of staff has been dismissed from National Trust Enterprises, the commercial arm of the charity, due to financial discrepancies discovered by the trust.'
She said the matter was in the hands of the police.