He is said to be dismayed at the level of central control exercised by senior Government officials and is known to be unhappy with the pace and direction of the post-16 reforms.
Mr Anderson, who was appointed by Ian Lang, the former Scottish Secretary, is also thought to be uneasy about the huge investment involved at a time of severe budget cuts for councils.
So far, the programme has cost the Government Pounds 5 million. Another Pounds 2.1 million is budgeted for the unit that promotes the reforms and a further Pounds 2.5 million is planned for staff development.
The 24-strong information and publicity group has been responsible for overseeing the stream of documents on Higher Still, testing parental opinion and investigating special needs provision. Mr Anderson is said to be disenchanted by what he sees as the sidelining of the group's efforts.
The breaking point has been a combination of the control exercised by the programme's development unit, based at Moray House Institute in Edinburgh, and the increasingly centralising powers of Scottish Office officials.
Despite this latest setback, the programme's managers believe that they are still on target to meet the August 1998 implementation date and have been encouraged by the 15,000 responses to the consultation exercise launched last autumn.
Of the 28 subject frameworks, only English and communication is being substantially revamped. By stepping up the pace of the development phase, the Government hopes to leave even more time for implementation.
The Scottish Examination Board has also recommended to the strategy group that Standard grade and Higher Still exams should be taken almost simultaneously and finish at the same time. The board has tested various patterns in May and June. This would give schools more teaching time after Easter and allow courses to reach their targeted 160 hours.
Higher Still planners have responded to concerns over teacher workload by producing a bank of assessment instruments. Teachers will be free to use the test items or continue existing methods of assessment.
One senior adviser says it is "nonsense" that teachers could be faced with teaching up to five levels of ability in one classroom. But planners admit it could take up to five years for schools to address the needs of all students.
A further series of documents will be published next month