After playing a key role in the establishment of the MPA with David Pitchford in 2011, Blackall went on secondment to the Department for Transport as programme director on the Thameslink Programme.
He rejoined the MPA in October 2013 as director of operations.
A Cabinet Office spokesperson said: “We expect to begin the search process of recruiting the new chief executive for the Major Projects Authority in due course. David Blackall has taken on the role in acting capacity.”