Under the deal approved by John O'Brien, the franchising director, passengers will receive benefits worth pounds 1.5m - less than half the pounds 3.43m in windfalls five of its directors will receive.
Passenger groups had called for the deal to be blocked after figures showed that Chiltern, which runs from London's Marylebone to Buckinghamshire, Oxfordshire and Birmingham, had the seventh-worst punctuality record in 1998.
Mr O'Brien said the takeover was in the best interests of passengers as it "includes strong incentives to improve performance, moves towards integrated transport and a greater voice for passengers".
Under a new punctuality regime Chiltern will pay pounds 200 for every train more than 20 minutes late, pounds 250 for trains that are half-an-hour late or part-cancelled, and pounds 300 for a cancelled service, although the penalties will only kick in after a benchmark of pounds 30,000 has been hit.
Other measures include free travel on some buses, cheaper family tickets, better station security and comfort and greater priority for travellers with disabilities. John Reid, the Transport Minister, welcomed the punctuality targets as "a clear indication of the way forward".
Under the pounds 6m deal, managing director Adrian Shooter sees his 17 per cent stake rise in value from pounds 50,000 to pounds 1.65m. He is selling half his stake, netting pounds 824,000, as is marketing director Alex Turner and production director Owen Edgington. Finance director Tony Allen gets pounds 544,000, and chairman Sir Richard Morris pounds 412,000.