David Edmonds, a director of the company that controls the Olympic Park, has given his resignation to the Mayor of London, Sadiq Khan.
Earlier this week, it emerged that the cost of converting the 2012 Games venue into a football stadium for West Ham United has risen from £272m to £323m.
Khan has launched an investigation into the spiralling cost.
David Goldstone, chief executive of the London Legacy Development Corporation, said: "David [Edmonds] has made an enormous contribution to the legacy of the London 2012 Games and he has helped to steer the organisation through some extremely challenging issues. We thank him for all his hard work and wish him well in the future."
This weeks controversy centres on the stadium's 'retractable' seats, which will cost £8m to move during the summer when the venue's use changes, a huge hike on the original estimate of £300,000.
In another development, The Guardian reports that the designated safety officer of the Olympic Stadium resigned in May after becoming concerned about the retractable seating and the structure of the lower tier. Chris Baker is understood to have quit shortly before a concert by AC/DC on 4 June.
The cost of converting the stadium for football has taken the bill to £752m, all of which has been met by the taxpayer apart from a £15m contribution from West Ham.